help with conf file

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help with conf file

Jayaraman, Pushkala

Hello after resolving issues with database access, I see that I get this when I try accessing gborwse2

http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

 

I am not able to see the overview/region/detail panels..

 

I know there is something wrong with the config file.. but I am just not sure what..

 

Herewith is my config file:

 

 

 

 

[GENERAL]

description   = Rat Genome V3.4 Assembly

db_adaptor    = Bio::DB::GFF

db_args       = -adaptor dbi::mysql

                -dsn     dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

                                -user rgdselect

                                -pass rgdselusrdv1a

 

# examples to show in the introduction

examples = proteinuria

           Grik1

           RGD620956

 

# Default track settings

[TRACK DEFAULTS]

glyph       = generic

height      = 8

bgcolor     = cyan

fgcolor     = cyan

font2color  = black

label density = 25

 

### Individual track settings ####

[PSEUDOGENE:overview]

category     = GENE MODELS

feature      = pseudogene:GenBank

glyph        = arrow

fgcolor      = blue

linewidth    = 2

height       = 6

link   = sub {

                  my $f=shift;

                  if ($f->attributes->{'Dbxref'} eq "") {

                      return;

                  }

                  my $xdb=join(",", @{$f->attributes->{Dbxref}});

                  my $ncbiId;

                  if ($xdb =~/GeneID:(\d+)/) {

                    $ncbiId=$1;

                  }

                  return "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

                }

key          =  Entrez Pseudogenes

citation     = This track shows pseudogenes labeled as such at <a href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a feature provides additional annotation including the EntrezGeneID, Name, Description, and Source. Clicking on a features links to the appropriate EntrezGene record.

 

 

 

I know there is absolutely nothing here..

But I am just not able to see the Overview/Region/detail panels or the glyphs.. I can see the section that allows you to search for keywords/click on what tracks you need ON/select datasource.

I can even see the Overview/Region/Detail sections when I chose some of the sample datasets provided eg Yeast Basic and yeast Advanced..

 

Where am I going wrong?

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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Re: [Gmod-gbrowse] help with conf file

Scott Cain
Hi Pushkala,

Are there any messages in the error log?

Scott




On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello after resolving issues with database access, I see that I get this
> when I try accessing gborwse2
>
> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>
>
>
> I am not able to see the overview/region/detail panels..
>
>
>
> I know there is something wrong with the config file.. but I am just not
> sure what..
>
>
>
> Herewith is my config file:
>
>
>
>
>
>
>
>
>
> [GENERAL]
>
> description   = Rat Genome V3.4 Assembly
>
> db_adaptor    = Bio::DB::GFF
>
> db_args       = -adaptor dbi::mysql
>
>                 -dsn
> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>
>                                 -user rgdselect
>
>                                 -pass rgdselusrdv1a
>
>
>
> # examples to show in the introduction
>
> examples = proteinuria
>
>            Grik1
>
>            RGD620956
>
>
>
> # Default track settings
>
> [TRACK DEFAULTS]
>
> glyph       = generic
>
> height      = 8
>
> bgcolor     = cyan
>
> fgcolor     = cyan
>
> font2color  = black
>
> label density = 25
>
>
>
> ### Individual track settings ####
>
> [PSEUDOGENE:overview]
>
> category     = GENE MODELS
>
> feature      = pseudogene:GenBank
>
> glyph        = arrow
>
> fgcolor      = blue
>
> linewidth    = 2
>
> height       = 6
>
> link   = sub {
>
>                   my $f=shift;
>
>                   if ($f->attributes->{'Dbxref'} eq "") {
>
>                       return;
>
>                   }
>
>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>
>                   my $ncbiId;
>
>                   if ($xdb =~/GeneID:(\d+)/) {
>
>                     $ncbiId=$1;
>
>                   }
>
>                   return
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>
>                 }
>
> key          =  Entrez Pseudogenes
>
> citation     = This track shows pseudogenes labeled as such at <a
> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a
> feature provides additional annotation including the EntrezGeneID, Name,
> Description, and Source. Clicking on a features links to the appropriate
> EntrezGene record.
>
>
>
>
>
>
>
> I know there is absolutely nothing here..
>
> But I am just not able to see the Overview/Region/detail panels or the
> glyphs.. I can see the section that allows you to search for keywords/click
> on what tracks you need ON/select datasource.
>
> I can even see the Overview/Region/Detail sections when I chose some of the
> sample datasets provided eg Yeast Basic and yeast Advanced..
>
>
>
> Where am I going wrong?
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
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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Re: [Gmod-gbrowse] help with conf file

Jayaraman, Pushkala
Nope! The error log seems to run as though nothing happened..


Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 1:35 PM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List; [hidden email]
Subject: Re: [Gmod-gbrowse] help with conf file

Hi Pushkala,

Are there any messages in the error log?

Scott




On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello after resolving issues with database access, I see that I get this
> when I try accessing gborwse2
>
> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>
>
>
> I am not able to see the overview/region/detail panels..
>
>
>
> I know there is something wrong with the config file.. but I am just not
> sure what..
>
>
>
> Herewith is my config file:
>
>
>
>
>
>
>
>
>
> [GENERAL]
>
> description   = Rat Genome V3.4 Assembly
>
> db_adaptor    = Bio::DB::GFF
>
> db_args       = -adaptor dbi::mysql
>
>                 -dsn
> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>
>                                 -user rgdselect
>
>                                 -pass rgdselusrdv1a
>
>
>
> # examples to show in the introduction
>
> examples = proteinuria
>
>            Grik1
>
>            RGD620956
>
>
>
> # Default track settings
>
> [TRACK DEFAULTS]
>
> glyph       = generic
>
> height      = 8
>
> bgcolor     = cyan
>
> fgcolor     = cyan
>
> font2color  = black
>
> label density = 25
>
>
>
> ### Individual track settings ####
>
> [PSEUDOGENE:overview]
>
> category     = GENE MODELS
>
> feature      = pseudogene:GenBank
>
> glyph        = arrow
>
> fgcolor      = blue
>
> linewidth    = 2
>
> height       = 6
>
> link   = sub {
>
>                   my $f=shift;
>
>                   if ($f->attributes->{'Dbxref'} eq "") {
>
>                       return;
>
>                   }
>
>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>
>                   my $ncbiId;
>
>                   if ($xdb =~/GeneID:(\d+)/) {
>
>                     $ncbiId=$1;
>
>                   }
>
>                   return
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>
>                 }
>
> key          =  Entrez Pseudogenes
>
> citation     = This track shows pseudogenes labeled as such at <a
> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a
> feature provides additional annotation including the EntrezGeneID, Name,
> Description, and Source. Clicking on a features links to the appropriate
> EntrezGene record.
>
>
>
>
>
>
>
> I know there is absolutely nothing here..
>
> But I am just not able to see the Overview/Region/detail panels or the
> glyphs.. I can see the section that allows you to search for keywords/click
> on what tracks you need ON/select datasource.
>
> I can even see the Overview/Region/Detail sections when I chose some of the
> sample datasets provided eg Yeast Basic and yeast Advanced..
>
>
>
> Where am I going wrong?
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
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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Re: [Gmod-gbrowse] help with conf file

Jayaraman, Pushkala
In reply to this post by Scott Cain
Hello,
I now have another problem...Keeping with the previous email.
I tried to change the schema from GFF to Seq Feature Store using this command:
bp_seqfeature_load.pl -c -f -a DBI::mysql -d "DBI::mysql:database=dev_904_pj;host=forte.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4 *.gff3

..and tried to create a new database and I get these error towards the end of loading the data into the Mysql database:

Building object tree... 8.54s80s
Loading bulk data into database...DBD::mysql::db do failed: The used command is not allowed with this MySQL version at /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 544, <GEN0> line 58750.

I tried once again and I get this error again:
Building object tree... 8.54s80s
bash: Building: command not found
<llowed with this MySQL version at /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 544, <GEN0> line 58750.                                      
bash: GEN0: No such file or directory


Our MYSQL database server version: 5.1.44-community MySQL Community Server (GPL). What is wrong with the command?

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 1:35 PM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List; [hidden email]
Subject: Re: [Gmod-gbrowse] help with conf file

Hi Pushkala,

Are there any messages in the error log?

Scott




On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello after resolving issues with database access, I see that I get this
> when I try accessing gborwse2
>
> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>
>
>
> I am not able to see the overview/region/detail panels..
>
>
>
> I know there is something wrong with the config file.. but I am just not
> sure what..
>
>
>
> Herewith is my config file:
>
>
>
>
>
>
>
>
>
> [GENERAL]
>
> description   = Rat Genome V3.4 Assembly
>
> db_adaptor    = Bio::DB::GFF
>
> db_args       = -adaptor dbi::mysql
>
>                 -dsn
> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>
>                                 -user rgdselect
>
>                                 -pass rgdselusrdv1a
>
>
>
> # examples to show in the introduction
>
> examples = proteinuria
>
>            Grik1
>
>            RGD620956
>
>
>
> # Default track settings
>
> [TRACK DEFAULTS]
>
> glyph       = generic
>
> height      = 8
>
> bgcolor     = cyan
>
> fgcolor     = cyan
>
> font2color  = black
>
> label density = 25
>
>
>
> ### Individual track settings ####
>
> [PSEUDOGENE:overview]
>
> category     = GENE MODELS
>
> feature      = pseudogene:GenBank
>
> glyph        = arrow
>
> fgcolor      = blue
>
> linewidth    = 2
>
> height       = 6
>
> link   = sub {
>
>                   my $f=shift;
>
>                   if ($f->attributes->{'Dbxref'} eq "") {
>
>                       return;
>
>                   }
>
>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>
>                   my $ncbiId;
>
>                   if ($xdb =~/GeneID:(\d+)/) {
>
>                     $ncbiId=$1;
>
>                   }
>
>                   return
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>
>                 }
>
> key          =  Entrez Pseudogenes
>
> citation     = This track shows pseudogenes labeled as such at <a
> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a
> feature provides additional annotation including the EntrezGeneID, Name,
> Description, and Source. Clicking on a features links to the appropriate
> EntrezGene record.
>
>
>
>
>
>
>
> I know there is absolutely nothing here..
>
> But I am just not able to see the Overview/Region/detail panels or the
> glyphs.. I can see the section that allows you to search for keywords/click
> on what tracks you need ON/select datasource.
>
> I can even see the Overview/Region/Detail sections when I chose some of the
> sample datasets provided eg Yeast Basic and yeast Advanced..
>
>
>
> Where am I going wrong?
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------

_______________________________________________
Gmod-devel mailing list
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Re: [Gmod-gbrowse] help with conf file

Scott Cain
In reply to this post by Jayaraman, Pushkala
If you remove the callback does it go back to working?

Scott


On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Nope! The error log seems to run as though nothing happened..
>
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, May 25, 2010 1:35 PM
> To: Jayaraman, Pushkala
> Cc: Gbrowse Mailing List; [hidden email]
> Subject: Re: [Gmod-gbrowse] help with conf file
>
> Hi Pushkala,
>
> Are there any messages in the error log?
>
> Scott
>
>
>
>
> On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Hello after resolving issues with database access, I see that I get this
>> when I try accessing gborwse2
>>
>> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>>
>>
>>
>> I am not able to see the overview/region/detail panels..
>>
>>
>>
>> I know there is something wrong with the config file.. but I am just not
>> sure what..
>>
>>
>>
>> Herewith is my config file:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> [GENERAL]
>>
>> description   = Rat Genome V3.4 Assembly
>>
>> db_adaptor    = Bio::DB::GFF
>>
>> db_args       = -adaptor dbi::mysql
>>
>>                 -dsn
>> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>>
>>                                 -user rgdselect
>>
>>                                 -pass rgdselusrdv1a
>>
>>
>>
>> # examples to show in the introduction
>>
>> examples = proteinuria
>>
>>            Grik1
>>
>>            RGD620956
>>
>>
>>
>> # Default track settings
>>
>> [TRACK DEFAULTS]
>>
>> glyph       = generic
>>
>> height      = 8
>>
>> bgcolor     = cyan
>>
>> fgcolor     = cyan
>>
>> font2color  = black
>>
>> label density = 25
>>
>>
>>
>> ### Individual track settings ####
>>
>> [PSEUDOGENE:overview]
>>
>> category     = GENE MODELS
>>
>> feature      = pseudogene:GenBank
>>
>> glyph        = arrow
>>
>> fgcolor      = blue
>>
>> linewidth    = 2
>>
>> height       = 6
>>
>> link   = sub {
>>
>>                   my $f=shift;
>>
>>                   if ($f->attributes->{'Dbxref'} eq "") {
>>
>>                       return;
>>
>>                   }
>>
>>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>>
>>                   my $ncbiId;
>>
>>                   if ($xdb =~/GeneID:(\d+)/) {
>>
>>                     $ncbiId=$1;
>>
>>                   }
>>
>>                   return
>> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>>
>>                 }
>>
>> key          =  Entrez Pseudogenes
>>
>> citation     = This track shows pseudogenes labeled as such at <a
>> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a
>> feature provides additional annotation including the EntrezGeneID, Name,
>> Description, and Source. Clicking on a features links to the appropriate
>> EntrezGene record.
>>
>>
>>
>>
>>
>>
>>
>> I know there is absolutely nothing here..
>>
>> But I am just not able to see the Overview/Region/detail panels or the
>> glyphs.. I can see the section that allows you to search for keywords/click
>> on what tracks you need ON/select datasource.
>>
>> I can even see the Overview/Region/Detail sections when I chose some of the
>> sample datasets provided eg Yeast Basic and yeast Advanced..
>>
>>
>>
>> Where am I going wrong?
>>
>>
>>
>> Pushkala Jayaraman
>>
>> Programmer/Analyst
>>
>> Rat Genome Database
>>
>> Human and Molecular Genetics Center
>>
>> Medical College of Wisconsin
>>
>> Email: [hidden email]
>>
>> Work: 414-955-2229
>>
>> www.rgd.mcw.edu
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
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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Gmod-devel mailing list
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Re: [Gmod-gbrowse] help with conf file

Scott Cain
In reply to this post by Jayaraman, Pushkala
Hi Pushkala,

Try adding this to your dsn: mysql_local_infile=1, like this:

  --dsn "DBI:mysql:mydb;mysql_local_infile=1"

This has been fixed (I think) in the development version of BioPerl.

Scott


On Tue, May 25, 2010 at 3:37 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello,
> I now have another problem...Keeping with the previous email.
> I tried to change the schema from GFF to Seq Feature Store using this command:
> bp_seqfeature_load.pl -c -f -a DBI::mysql -d "DBI::mysql:database=dev_904_pj;host=forte.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4 *.gff3
>
> ..and tried to create a new database and I get these error towards the end of loading the data into the Mysql database:
>
> Building object tree... 8.54s80s
> Loading bulk data into database...DBD::mysql::db do failed: The used command is not allowed with this MySQL version at /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 544, <GEN0> line 58750.
>
> I tried once again and I get this error again:
> Building object tree... 8.54s80s
> bash: Building: command not found
> <llowed with this MySQL version at /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 544, <GEN0> line 58750.
> bash: GEN0: No such file or directory
>
>
> Our MYSQL database server version: 5.1.44-community MySQL Community Server (GPL). What is wrong with the command?
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, May 25, 2010 1:35 PM
> To: Jayaraman, Pushkala
> Cc: Gbrowse Mailing List; [hidden email]
> Subject: Re: [Gmod-gbrowse] help with conf file
>
> Hi Pushkala,
>
> Are there any messages in the error log?
>
> Scott
>
>
>
>
> On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Hello after resolving issues with database access, I see that I get this
>> when I try accessing gborwse2
>>
>> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>>
>>
>>
>> I am not able to see the overview/region/detail panels..
>>
>>
>>
>> I know there is something wrong with the config file.. but I am just not
>> sure what..
>>
>>
>>
>> Herewith is my config file:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> [GENERAL]
>>
>> description   = Rat Genome V3.4 Assembly
>>
>> db_adaptor    = Bio::DB::GFF
>>
>> db_args       = -adaptor dbi::mysql
>>
>>                 -dsn
>> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>>
>>                                 -user rgdselect
>>
>>                                 -pass rgdselusrdv1a
>>
>>
>>
>> # examples to show in the introduction
>>
>> examples = proteinuria
>>
>>            Grik1
>>
>>            RGD620956
>>
>>
>>
>> # Default track settings
>>
>> [TRACK DEFAULTS]
>>
>> glyph       = generic
>>
>> height      = 8
>>
>> bgcolor     = cyan
>>
>> fgcolor     = cyan
>>
>> font2color  = black
>>
>> label density = 25
>>
>>
>>
>> ### Individual track settings ####
>>
>> [PSEUDOGENE:overview]
>>
>> category     = GENE MODELS
>>
>> feature      = pseudogene:GenBank
>>
>> glyph        = arrow
>>
>> fgcolor      = blue
>>
>> linewidth    = 2
>>
>> height       = 6
>>
>> link   = sub {
>>
>>                   my $f=shift;
>>
>>                   if ($f->attributes->{'Dbxref'} eq "") {
>>
>>                       return;
>>
>>                   }
>>
>>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>>
>>                   my $ncbiId;
>>
>>                   if ($xdb =~/GeneID:(\d+)/) {
>>
>>                     $ncbiId=$1;
>>
>>                   }
>>
>>                   return
>> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>>
>>                 }
>>
>> key          =  Entrez Pseudogenes
>>
>> citation     = This track shows pseudogenes labeled as such at <a
>> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a
>> feature provides additional annotation including the EntrezGeneID, Name,
>> Description, and Source. Clicking on a features links to the appropriate
>> EntrezGene record.
>>
>>
>>
>>
>>
>>
>>
>> I know there is absolutely nothing here..
>>
>> But I am just not able to see the Overview/Region/detail panels or the
>> glyphs.. I can see the section that allows you to search for keywords/click
>> on what tracks you need ON/select datasource.
>>
>> I can even see the Overview/Region/Detail sections when I chose some of the
>> sample datasets provided eg Yeast Basic and yeast Advanced..
>>
>>
>>
>> Where am I going wrong?
>>
>>
>>
>> Pushkala Jayaraman
>>
>> Programmer/Analyst
>>
>> Rat Genome Database
>>
>> Human and Molecular Genetics Center
>>
>> Medical College of Wisconsin
>>
>> Email: [hidden email]
>>
>> Work: 414-955-2229
>>
>> www.rgd.mcw.edu
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
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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Re: [Gmod-gbrowse] help with conf file

Jayaraman, Pushkala
In reply to this post by Scott Cain

I'm trying to load the database by removing the -f feature.. I will add the local parameter and check.. I did read about it in the forums but did not think it necessary for my database as I never added it for the database on localhost.

Although, even with SeqFeature Store, I do not see the overview region or the details panel

 

Herewith is attached a picture: If you see the picture on the right screen, You will notice that there is no scale..

How do it rectify this?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 3:30 PM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List; [hidden email]
Subject: Re: [Gmod-gbrowse] help with conf file

 

If you remove the callback does it go back to working?

 

Scott

 

 

On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Nope! The error log seems to run as though nothing happened..

> 

> 

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> 

> 

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 1:35 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> 

> Hi Pushkala,

> 

> Are there any messages in the error log?

> 

> Scott

> 

> 

> 

> 

> On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:

>> Hello after resolving issues with database access, I see that I get this

>> when I try accessing gborwse2

>> 

>> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

>> 

>> 

>> 

>> I am not able to see the overview/region/detail panels..

>> 

>> 

>> 

>> I know there is something wrong with the config file.. but I am just not

>> sure what..

>> 

>> 

>> 

>> Herewith is my config file:

>> 

>> 

>> 

>> 

>> 

>> 

>> 

>> 

>> 

>> [GENERAL]

>> 

>> description   = Rat Genome V3.4 Assembly

>> 

>> db_adaptor    = Bio::DB::GFF

>> 

>> db_args       = -adaptor dbi::mysql

>> 

>>                 -dsn

>> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

>> 

>>                                 -user rgdselect

>> 

>>                                 -pass rgdselusrdv1a

>> 

>> 

>> 

>> # examples to show in the introduction

>> 

>> examples = proteinuria

>> 

>>            Grik1

>> 

>>            RGD620956

>> 

>> 

>> 

>> # Default track settings

>> 

>> [TRACK DEFAULTS]

>> 

>> glyph       = generic

>> 

>> height      = 8

>> 

>> bgcolor     = cyan

>> 

>> fgcolor     = cyan

>> 

>> font2color  = black

>> 

>> label density = 25

>> 

>> 

>> 

>> ### Individual track settings ####

>> 

>> [PSEUDOGENE:overview]

>> 

>> category     = GENE MODELS

>> 

>> feature      = pseudogene:GenBank

>> 

>> glyph        = arrow

>> 

>> fgcolor      = blue

>> 

>> linewidth    = 2

>> 

>> height       = 6

>> 

>> link   = sub {

>> 

>>                   my $f=shift;

>> 

>>                   if ($f->attributes->{'Dbxref'} eq "") {

>> 

>>                       return;

>> 

>>                   }

>> 

>>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

>> 

>>                   my $ncbiId;

>> 

>>                   if ($xdb =~/GeneID:(\d+)/) {

>> 

>>                     $ncbiId=$1;

>> 

>>                   }

>> 

>>                   return

>> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

>> 

>>                 }

>> 

>> key          =  Entrez Pseudogenes

>> 

>> citation     = This track shows pseudogenes labeled as such at <a

>> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a

>> feature provides additional annotation including the EntrezGeneID, Name,

>> Description, and Source. Clicking on a features links to the appropriate

>> EntrezGene record.

>> 

>> 

>> 

>> 

>> 

>> 

>> 

>> I know there is absolutely nothing here..

>> 

>> But I am just not able to see the Overview/Region/detail panels or the

>> glyphs.. I can see the section that allows you to search for keywords/click

>> on what tracks you need ON/select datasource.

>> 

>> I can even see the Overview/Region/Detail sections when I chose some of the

>> sample datasets provided eg Yeast Basic and yeast Advanced..

>> 

>> 

>> 

>> Where am I going wrong?

>> 

>> 

>> 

>> Pushkala Jayaraman

>> 

>> Programmer/Analyst

>> 

>> Rat Genome Database

>> 

>> Human and Molecular Genetics Center

>> 

>> Medical College of Wisconsin

>> 

>> Email: [hidden email]

>> 

>> Work: 414-955-2229

>> 

>> www.rgd.mcw.edu

>> 

>> 

>> 

>> ------------------------------------------------------------------------------

>> 

>> 

>> _______________________________________________

>> Gmod-gbrowse mailing list

>> [hidden email]

>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>> 

>> 

> 

> 

> 

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> 

 

 

 

--

------------------------------------------------------------------------

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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|

Re: [Gmod-gbrowse] help with conf file

Ram Podicheti
Pushkala,
I am not sure how pertinent my message would be to your problem, but I
noticed something weird in the way GBrowse handles certain GFF3 files.
At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides
the 'ID' in the line representing the reference sequence.

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

If the Name is omitted, you may get the 'landmark not recognized' error.
Please note that this is not always the case, hence I called it 'weird'.
Moreover, I thought 'Name' is meant to provide only a label and not
required by GBrowse to identify the seqid.

So, try giving a Name besides the ID and see how that goes.
Cheers,

Ram


Jayaraman, Pushkala wrote:

>
> I'm trying to load the database by removing the -f feature.. I will
> add the local parameter and check.. I did read about it in the forums
> but did not think it necessary for my database as I never added it for
> the database on localhost.
>
> Although, even with SeqFeature Store, I do not see the overview region
> or the details panel
>
>  
>
> Herewith is attached a picture: If you see the picture on the right
> screen, You will notice that there is no scale..
>
> How do it rectify this?
>
>  
>
>  
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>  
>
>  
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, May 25, 2010 3:30 PM
> To: Jayaraman, Pushkala
> Cc: Gbrowse Mailing List; [hidden email]
> Subject: Re: [Gmod-gbrowse] help with conf file
>
>  
>
> If you remove the callback does it go back to working?
>
>  
>
> Scott
>
>  
>
>  
>
> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala
> <[hidden email]> wrote:
>
> > Nope! The error log seems to run as though nothing happened..
>
> >
>
> >
>
> > Pushkala Jayaraman
>
> > Programmer/Analyst
>
> > Rat Genome Database
>
> > Human and Molecular Genetics Center
>
> > Medical College of Wisconsin
>
> > Email: [hidden email]
>
> > Work: 414-955-2229
>
> > www.rgd.mcw.edu
>
> >
>
> >
>
> > -----Original Message-----
>
> > From: Scott Cain [mailto:[hidden email]]
>
> > Sent: Tuesday, May 25, 2010 1:35 PM
>
> > To: Jayaraman, Pushkala
>
> > Cc: Gbrowse Mailing List; [hidden email]
>
> > Subject: Re: [Gmod-gbrowse] help with conf file
>
> >
>
> > Hi Pushkala,
>
> >
>
> > Are there any messages in the error log?
>
> >
>
> > Scott
>
> >
>
> >
>
> >
>
> >
>
> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala
> <[hidden email]> wrote:
>
> >> Hello after resolving issues with database access, I see that I get
> this
>
> >> when I try accessing gborwse2
>
> >>
>
> >>
> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>
> >>
>
> >>
>
> >>
>
> >> I am not able to see the overview/region/detail panels..
>
> >>
>
> >>
>
> >>
>
> >> I know there is something wrong with the config file.. but I am
> just not
>
> >> sure what..
>
> >>
>
> >>
>
> >>
>
> >> Herewith is my config file:
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> [GENERAL]
>
> >>
>
> >> description   = Rat Genome V3.4 Assembly
>
> >>
>
> >> db_adaptor    = Bio::DB::GFF
>
> >>
>
> >> db_args       = -adaptor dbi::mysql
>
> >>
>
> >>                 -dsn
>
> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>
> >>
>
> >>                                 -user rgdselect
>
> >>
>
> >>                                 -pass rgdselusrdv1a
>
> >>
>
> >>
>
> >>
>
> >> # examples to show in the introduction
>
> >>
>
> >> examples = proteinuria
>
> >>
>
> >>            Grik1
>
> >>
>
> >>            RGD620956
>
> >>
>
> >>
>
> >>
>
> >> # Default track settings
>
> >>
>
> >> [TRACK DEFAULTS]
>
> >>
>
> >> glyph       = generic
>
> >>
>
> >> height      = 8
>
> >>
>
> >> bgcolor     = cyan
>
> >>
>
> >> fgcolor     = cyan
>
> >>
>
> >> font2color  = black
>
> >>
>
> >> label density = 25
>
> >>
>
> >>
>
> >>
>
> >> ### Individual track settings ####
>
> >>
>
> >> [PSEUDOGENE:overview]
>
> >>
>
> >> category     = GENE MODELS
>
> >>
>
> >> feature      = pseudogene:GenBank
>
> >>
>
> >> glyph        = arrow
>
> >>
>
> >> fgcolor      = blue
>
> >>
>
> >> linewidth    = 2
>
> >>
>
> >> height       = 6
>
> >>
>
> >> link   = sub {
>
> >>
>
> >>                   my $f=shift;
>
> >>
>
> >>                   if ($f->attributes->{'Dbxref'} eq "") {
>
> >>
>
> >>                       return;
>
> >>
>
> >>                   }
>
> >>
>
> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>
> >>
>
> >>                   my $ncbiId;
>
> >>
>
> >>                   if ($xdb =~/GeneID:(\d+)/) {
>
> >>
>
> >>                     $ncbiId=$1;
>
> >>
>
> >>                   }
>
> >>
>
> >>                   return
>
> >>
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>
> >>
>
> >>                 }
>
> >>
>
> >> key          =  Entrez Pseudogenes
>
> >>
>
> >> citation     = This track shows pseudogenes labeled as such at <a
>
> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering
> over a
>
> >> feature provides additional annotation including the EntrezGeneID,
> Name,
>
> >> Description, and Source. Clicking on a features links to the
> appropriate
>
> >> EntrezGene record.
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> I know there is absolutely nothing here..
>
> >>
>
> >> But I am just not able to see the Overview/Region/detail panels or the
>
> >> glyphs.. I can see the section that allows you to search for
> keywords/click
>
> >> on what tracks you need ON/select datasource.
>
> >>
>
> >> I can even see the Overview/Region/Detail sections when I chose
> some of the
>
> >> sample datasets provided eg Yeast Basic and yeast Advanced..
>
> >>
>
> >>
>
> >>
>
> >> Where am I going wrong?
>
> >>
>
> >>
>
> >>
>
> >> Pushkala Jayaraman
>
> >>
>
> >> Programmer/Analyst
>
> >>
>
> >> Rat Genome Database
>
> >>
>
> >> Human and Molecular Genetics Center
>
> >>
>
> >> Medical College of Wisconsin
>
> >>
>
> >> Email: [hidden email]
>
> >>
>
> >> Work: 414-955-2229
>
> >>
>
> >> www.rgd.mcw.edu
>
> >>
>
> >>
>
> >>
>
> >>
> ------------------------------------------------------------------------------
>
> >>
>
> >>
>
> >> _______________________________________________
>
> >> Gmod-gbrowse mailing list
>
> >> [hidden email]
>
> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> >>
>
> >>
>
> >
>
> >
>
> >
>
> > --
>
> > ------------------------------------------------------------------------
>
> > Scott Cain, Ph. D.                                   scott at
> scottcain dot net
>
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>
> > Ontario Institute for Cancer Research
>
> >
>
>  
>
>  
>
>  
>
> --
>
> ------------------------------------------------------------------------
>
> Scott Cain, Ph. D.                                   scott at
> scottcain dot net
>
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>
>  
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>  


------------------------------------------------------------------------------

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Re: [Gmod-gbrowse] help with conf file

Jayaraman, Pushkala

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> 

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> 

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> 

> 

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> 

> How do it rectify this?

> 

> 

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst

> 

> Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> Email: [hidden email]

> 

> Work: 414-955-2229

> 

> www.rgd.mcw.edu

> 

> 

> 

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> 

> 

> If you remove the callback does it go back to working?

> 

> 

> Scott

> 

> 

> 

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> 

> > Nope! The error log seems to run as though nothing happened..

> 

> >

> 

> >

> 

> > Pushkala Jayaraman

> 

> > Programmer/Analyst

> 

> > Rat Genome Database

> 

> > Human and Molecular Genetics Center

> 

> > Medical College of Wisconsin

> 

> > Email: [hidden email]

> 

> > Work: 414-955-2229

> 

> > www.rgd.mcw.edu

> 

> >

> 

> >

> 

> > -----Original Message-----

> 

> > From: Scott Cain [mailto:[hidden email]]

> 

> > Sent: Tuesday, May 25, 2010 1:35 PM

> 

> > To: Jayaraman, Pushkala

> 

> > Cc: Gbrowse Mailing List; [hidden email]

> 

> > Subject: Re: [Gmod-gbrowse] help with conf file

> 

> >

> 

> > Hi Pushkala,

> 

> >

> 

> > Are there any messages in the error log?

> 

> >

> 

> > Scott

> 

> >

> 

> >

> 

> >

> 

> >

> 

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> 

> >> Hello after resolving issues with database access, I see that I get

> this

> 

> >> when I try accessing gborwse2

> 

> >>

> 

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> 

> >>

> 

> >>

> 

> >>

> 

> >> I am not able to see the overview/region/detail panels..

> 

> >>

> 

> >>

> 

> >>

> 

> >> I know there is something wrong with the config file.. but I am

> just not

> 

> >> sure what..

> 

> >>

> 

> >>

> 

> >>

> 

> >> Herewith is my config file:

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >> [GENERAL]

> 

> >>

> 

> >> description   = Rat Genome V3.4 Assembly

> 

> >>

> 

> >> db_adaptor    = Bio::DB::GFF

> 

> >>

> 

> >> db_args       = -adaptor dbi::mysql

> 

> >>

> 

> >>                 -dsn

> 

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> 

> >>

> 

> >>                                 -user rgdselect

> 

> >>

> 

> >>                                 -pass rgdselusrdv1a

> 

> >>

> 

> >>

> 

> >>

> 

> >> # examples to show in the introduction

> 

> >>

> 

> >> examples = proteinuria

> 

> >>

> 

> >>            Grik1

> 

> >>

> 

> >>            RGD620956

> 

> >>

> 

> >>

> 

> >>

> 

> >> # Default track settings

> 

> >>

> 

> >> [TRACK DEFAULTS]

> 

> >>

> 

> >> glyph       = generic

> 

> >>

> 

> >> height      = 8

> 

> >>

> 

> >> bgcolor     = cyan

> 

> >>

> 

> >> fgcolor     = cyan

> 

> >>

> 

> >> font2color  = black

> 

> >>

> 

> >> label density = 25

> 

> >>

> 

> >>

> 

> >>

> 

> >> ### Individual track settings ####

> 

> >>

> 

> >> [PSEUDOGENE:overview]

> 

> >>

> 

> >> category     = GENE MODELS

> 

> >>

> 

> >> feature      = pseudogene:GenBank

> 

> >>

> 

> >> glyph        = arrow

> 

> >>

> 

> >> fgcolor      = blue

> 

> >>

> 

> >> linewidth    = 2

> 

> >>

> 

> >> height       = 6

> 

> >>

> 

> >> link   = sub {

> 

> >>

> 

> >>                   my $f=shift;

> 

> >>

> 

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> 

> >>

> 

> >>                       return;

> 

> >>

> 

> >>                   }

> 

> >>

> 

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> 

> >>

> 

> >>                   my $ncbiId;

> 

> >>

> 

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> 

> >>

> 

> >>                     $ncbiId=$1;

> 

> >>

> 

> >>                   }

> 

> >>

> 

> >>                   return

> 

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> 

> >>

> 

> >>                 }

> 

> >>

> 

> >> key          =  Entrez Pseudogenes

> 

> >>

> 

> >> citation     = This track shows pseudogenes labeled as such at <a

> 

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> 

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> 

> >> Description, and Source. Clicking on a features links to the

> appropriate

> 

> >> EntrezGene record.

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >> I know there is absolutely nothing here..

> 

> >>

> 

> >> But I am just not able to see the Overview/Region/detail panels or the

> 

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> 

> >> on what tracks you need ON/select datasource.

> 

> >>

> 

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> 

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> 

> >>

> 

> >>

> 

> >>

> 

> >> Where am I going wrong?

> 

> >>

> 

> >>

> 

> >>

> 

> >> Pushkala Jayaraman

> 

> >>

> 

> >> Programmer/Analyst

> 

> >>

> 

> >> Rat Genome Database

> 

> >>

> 

> >> Human and Molecular Genetics Center

> 

> >>

> 

> >> Medical College of Wisconsin

> 

> >>

> 

> >> Email: [hidden email]

> 

> >>

> 

> >> Work: 414-955-2229

> 

> >>

> 

> >> www.rgd.mcw.edu

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> ------------------------------------------------------------------------------

> 

> >>

> 

> >>

> 

> >> _______________________________________________

> 

> >> Gmod-gbrowse mailing list

> 

> >> [hidden email]

> 

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> 

> >>

> 

> >>

> 

> >

> 

> >

> 

> >

> 

> > --

> 

> > ------------------------------------------------------------------------

> 

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> 

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> 

> > Ontario Institute for Cancer Research

> 

> >

> 

> 

> 

> 

> --

> 

> ------------------------------------------------------------------------

> 

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> 

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> 

> Ontario Institute for Cancer Research

> 

> ------------------------------------------------------------------------

> 

> ------------------------------------------------------------------------------

> 

>  

> ------------------------------------------------------------------------

> 

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-gbrowse] help with conf file

Jayaraman, Pushkala

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> 

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> 

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> 

> 

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> 

> How do it rectify this?

> 

> 

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst

> 

> Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> Email: [hidden email]

> 

> Work: 414-955-2229

> 

> www.rgd.mcw.edu

> 

> 

> 

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> 

> 

> If you remove the callback does it go back to working?

> 

> 

> Scott

> 

> 

> 

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> 

> > Nope! The error log seems to run as though nothing happened..

> 

> >

> 

> >

> 

> > Pushkala Jayaraman

> 

> > Programmer/Analyst

> 

> > Rat Genome Database

> 

> > Human and Molecular Genetics Center

> 

> > Medical College of Wisconsin

> 

> > Email: [hidden email]

> 

> > Work: 414-955-2229

> 

> > www.rgd.mcw.edu

> 

> >

> 

> >

> 

> > -----Original Message-----

> 

> > From: Scott Cain [mailto:[hidden email]]

> 

> > Sent: Tuesday, May 25, 2010 1:35 PM

> 

> > To: Jayaraman, Pushkala

> 

> > Cc: Gbrowse Mailing List; [hidden email]

> 

> > Subject: Re: [Gmod-gbrowse] help with conf file

> 

> >

> 

> > Hi Pushkala,

> 

> >

> 

> > Are there any messages in the error log?

> 

> >

> 

> > Scott

> 

> >

> 

> >

> 

> >

> 

> >

> 

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> 

> >> Hello after resolving issues with database access, I see that I get

> this

> 

> >> when I try accessing gborwse2

> 

> >>

> 

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> 

> >>

> 

> >>

> 

> >>

> 

> >> I am not able to see the overview/region/detail panels..

> 

> >>

> 

> >>

> 

> >>

> 

> >> I know there is something wrong with the config file.. but I am

> just not

> 

> >> sure what..

> 

> >>

> 

> >>

> 

> >>

> 

> >> Herewith is my config file:

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >> [GENERAL]

> 

> >>

> 

> >> description   = Rat Genome V3.4 Assembly

> 

> >>

> 

> >> db_adaptor    = Bio::DB::GFF

> 

> >>

> 

> >> db_args       = -adaptor dbi::mysql

> 

> >>

> 

> >>                 -dsn

> 

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> 

> >>

> 

> >>                                 -user rgdselect

> 

> >>

> 

> >>                                 -pass rgdselusrdv1a

> 

> >>

> 

> >>

> 

> >>

> 

> >> # examples to show in the introduction

> 

> >>

> 

> >> examples = proteinuria

> 

> >>

> 

> >>            Grik1

> 

> >>

> 

> >>            RGD620956

> 

> >>

> 

> >>

> 

> >>

> 

> >> # Default track settings

> 

> >>

> 

> >> [TRACK DEFAULTS]

> 

> >>

> 

> >> glyph       = generic

> 

> >>

> 

> >> height      = 8

> 

> >>

> 

> >> bgcolor     = cyan

> 

> >>

> 

> >> fgcolor     = cyan

> 

> >>

> 

> >> font2color  = black

> 

> >>

> 

> >> label density = 25

> 

> >>

> 

> >>

> 

> >>

> 

> >> ### Individual track settings ####

> 

> >>

> 

> >> [PSEUDOGENE:overview]

> 

> >>

> 

> >> category     = GENE MODELS

> 

> >>

> 

> >> feature      = pseudogene:GenBank

> 

> >>

> 

> >> glyph        = arrow

> 

> >>

> 

> >> fgcolor      = blue

> 

> >>

> 

> >> linewidth    = 2

> 

> >>

> 

> >> height       = 6

> 

> >>

> 

> >> link   = sub {

> 

> >>

> 

> >>                   my $f=shift;

> 

> >>

> 

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> 

> >>

> 

> >>                       return;

> 

> >>

> 

> >>                   }

> 

> >>

> 

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> 

> >>

> 

> >>                   my $ncbiId;

> 

> >>

> 

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> 

> >>

> 

> >>                     $ncbiId=$1;

> 

> >>

> 

> >>                   }

> 

> >>

> 

> >>                   return

> 

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> 

> >>

> 

> >>                 }

> 

> >>

> 

> >> key          =  Entrez Pseudogenes

> 

> >>

> 

> >> citation     = This track shows pseudogenes labeled as such at <a

> 

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> 

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> 

> >> Description, and Source. Clicking on a features links to the

> appropriate

> 

> >> EntrezGene record.

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> 

> >> I know there is absolutely nothing here..

> 

> >>

> 

> >> But I am just not able to see the Overview/Region/detail panels or the

> 

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> 

> >> on what tracks you need ON/select datasource.

> 

> >>

> 

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> 

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> 

> >>

> 

> >>

> 

> >>

> 

> >> Where am I going wrong?

> 

> >>

> 

> >>

> 

> >>

> 

> >> Pushkala Jayaraman

> 

> >>

> 

> >> Programmer/Analyst

> 

> >>

> 

> >> Rat Genome Database

> 

> >>

> 

> >> Human and Molecular Genetics Center

> 

> >>

> 

> >> Medical College of Wisconsin

> 

> >>

> 

> >> Email: [hidden email]

> 

> >>

> 

> >> Work: 414-955-2229

> 

> >>

> 

> >> www.rgd.mcw.edu

> 

> >>

> 

> >>

> 

> >>

> 

> >>

> ------------------------------------------------------------------------------

> 

> >>

> 

> >>

> 

> >> _______________________________________________

> 

> >> Gmod-gbrowse mailing list

> 

> >> [hidden email]

> 

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> 

> >>

> 

> >>

> 

> >

> 

> >

> 

> >

> 

> > --

> 

> > ------------------------------------------------------------------------

> 

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> 

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> 

> > Ontario Institute for Cancer Research

> 

> >

> 

> 

> 

> 

> --

> 

> ------------------------------------------------------------------------

> 

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> 

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> 

> Ontario Institute for Cancer Research

> 

> ------------------------------------------------------------------------

> 

> ------------------------------------------------------------------------------

> 

>  

> ------------------------------------------------------------------------

> 

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-gbrowse] help with conf file

Scott Cain
Hi Pushkala,

Things that I would check:

1. Since the section that has gone missing contains the source list that is obtained from GBrowse.conf, make sure that that section of the configuration file is OK.

2.  The other thing in the section that could cause problems is plugins: remove any plugins from GBrowse.conf until everything gets sorted out and working again.

3. While I don't know if it matters, I would suggest that you change your configuration file to look more like the sample yeast_simple.conf: put the database connection info in to its own stanza after the general stuff in the conf file.

Scott


On Tue, May 25, 2010 at 6:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


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Gmod-devel mailing list
[hidden email]
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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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Re: [Gmod-gbrowse] help with conf file

Lincoln Stein
In reply to this post by Jayaraman, Pushkala
It looks to me as though you simply have not defined the chromosomes and their lengths in the database. As Scott said, you need to load a GFF3 file that has a series of Chromosome lines like this one:

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

Lincoln

On Tue, May 25, 2010 at 2:18 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


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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]>

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Re: [Gmod-gbrowse] help with conf file

Lincoln Stein
In reply to this post by Jayaraman, Pushkala
This is the expected behavior when you are not viewing a region.

Lincoln

On Tue, May 25, 2010 at 3:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


_______________________________________________
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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: [Gmod-gbrowse] help with conf file

Ram Podicheti
Is it normal for GBrowse to expect both ID and Name attributes for SeqID? Most of the standard gff datasets, including those from NCBI, that I have noticed make sure that both the attributes are included. Is Name not meant for supplying a visual element in the form of label alone?
Thanks,
 
Ram

On Tue, May 25, 2010 at 8:27 PM, Lincoln Stein <[hidden email]> wrote:
This is the expected behavior when you are not viewing a region.

Lincoln


On Tue, May 25, 2010 at 3:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


_______________________________________________
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]>


------------------------------------------------------------------------------


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|

Re: [Gmod-gbrowse] help with conf file

Scott Cain
Hi Ram,

Name is used for what you would call a feature; that is, what you would search for if you were looking for that feature, so you should definitely have Name=chr1.  ID is a little more fuzzy; while it shouldn't be required, in older releases of Bio::DB::SeqFeature::Store, I think there may have been times when it was required, but according to the spec, it shouldn't be.

Scott


On Tue, May 25, 2010 at 8:37 PM, Ram Podicheti <[hidden email]> wrote:
Is it normal for GBrowse to expect both ID and Name attributes for SeqID? Most of the standard gff datasets, including those from NCBI, that I have noticed make sure that both the attributes are included. Is Name not meant for supplying a visual element in the form of label alone?
Thanks,
 
Ram

On Tue, May 25, 2010 at 8:27 PM, Lincoln Stein <[hidden email]> wrote:
This is the expected behavior when you are not viewing a region.

Lincoln


On Tue, May 25, 2010 at 3:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


_______________________________________________
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]>


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
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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Gbrowse 2.07 not displaying

Smithies, Russell
I've got a fresh installation of GBrowse 2.07 and I can't work out why it's not working :-(
It installed OK with no error messages but I'm getting a http 500 error and the error messages are:


[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 292, <DATA> line 192.
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Odd number of elements in hash assignment at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Session.pm line 31, <DATA> line 192.
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Use of uninitialized value in list assignment at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Session.pm line 31, <DATA> line 192.
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Invalid source yeast_advanced at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 61
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 292, <DATA> line 192.
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 69, <DATA> line 192.
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] path_type must be one of 'config','htdocs', or 'url' at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 70
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] \tBio::Graphics::Browser2::resolve_path('Bio::Graphics::Browser2=HASH(0x21e13eb0)', 'config') called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 263
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] \tBio::Graphics::Browser2::data_source_path('Bio::Graphics::Browser2=HASH(0x21e13eb0)', 'undef') called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 269
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] \tBio::Graphics::Browser2::create_data_source('Bio::Graphics::Browser2=HASH(0x21e13eb0)', 'undef') called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 62
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] \tBio::Graphics::Browser2::Render::new('Bio::Graphics::Browser2::Render::HTML', 'Bio::Graphics::Browser2=HASH(0x21e13eb0)') called at /var/www/gbrowse2/cgi-bin/gbrowse line 43
[Wed May 26 15:04:48 2010] [error] [client 147.158.129.160] Premature end of script headers: gbrowse


Any ideas where I should look?
I think it's the path_type stuff in B::G::Browser2 but not sure why.
It's using the default configuration.

Thanx,

Russell Smithies
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Re: [Gmod-gbrowse] help with conf file

Ram Podicheti
In reply to this post by Scott Cain
Thanks Scott, that makes a whole lot sense - Name is required for that landmark to be found.
Thanks,
 
Ram

On Tue, May 25, 2010 at 10:54 PM, Scott Cain <[hidden email]> wrote:
Hi Ram,

Name is used for what you would call a feature; that is, what you would search for if you were looking for that feature, so you should definitely have Name=chr1.  ID is a little more fuzzy; while it shouldn't be required, in older releases of Bio::DB::SeqFeature::Store, I think there may have been times when it was required, but according to the spec, it shouldn't be.

Scott



On Tue, May 25, 2010 at 8:37 PM, Ram Podicheti <[hidden email]> wrote:
Is it normal for GBrowse to expect both ID and Name attributes for SeqID? Most of the standard gff datasets, including those from NCBI, that I have noticed make sure that both the attributes are included. Is Name not meant for supplying a visual element in the form of label alone?
Thanks,
 
Ram

On Tue, May 25, 2010 at 8:27 PM, Lincoln Stein <[hidden email]> wrote:
This is the expected behavior when you are not viewing a region.

Lincoln


On Tue, May 25, 2010 at 3:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


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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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------------------------------------------------------------------------
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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Re: [Gmod-gbrowse] help with conf file

Jayaraman, Pushkala

Hello,

You guys were right about the gff3 files needing the ID and the Name attribute.

But does it need that in a certain order? I am loading gff3 files for miRNA which have both the ID and the name attribute but not in the right order and yet it seems to hshwo the same error:

 

##gff-version 3

Chr1  miRBase     miRNA 56486969    56487038    .     +     .     Name=rno-mir-99b;ID=MI0000884

Chr1  miRBase     miRNA 56487134    56487226    .     +     .     Name=rno-let-7e;ID=MI0000832

Chr1  miRBase     miRNA 56487580    56487664    .     +     .     Name=rno-mir-125a;ID=MI0000895

Chr1  miRBase     miRNA 64068767    64068857    .     -     .     Name=rno-mir-935;ID=MI0012607

Chr1  miRBase     miRNA 64272844    64272924    .     -     .     Name=rno-mir-295;ID=MI0012611

Chr1  miRBase     miRNA 64272967    64273037    .     -     .     Name=rno-mir-294;ID=MI0012610

Chr1  miRBase     miRNA 64273328    64273399    .     -     .     Name=rno-mir-293;ID=MI0012609

Chr1  miRBase     miRNA 64274340    64274421    .     -     .     Name=rno-mir-292;ID=MI0000966

Chr1  miRBase     miRNA 64274628    64274709    .     -     .     Name=rno-mir-291a;ID=MI0000965

Chr1  miRBase     miRNA 64274926    64275006    .     -     .     Name=rno-mir-290;ID=MI0000964

Chr1  miRBase     miRNA 73183804    73183884    .     +     .     Name=rno-mir-295;ID=MI0012611

Chr1  miRBase     miRNA 78544318    78544414    .     +     .     Name=rno-mir-330;ID=MI0000606

Chr1  miRBase     miRNA 78904571    78904663    .     +     .     Name=rno-mir-343;ID=MI0000628

Chr1  miRBase     miRNA 95596077    95596161    .     +     .     Name=rno-mir-150;ID=MI0000920

Chr1  miRBase     miRNA 116020984   116021081   .     -     .     Name=rno-mir-344-1;ID=MI0000629

Chr1  miRBase     miRNA 118642399   118642504   .     +     .     Name=rno-mir-211;ID=MI0000951

Chr1  miRBase     miRNA 134607264   134607358   .     +     .     Name=rno-mir-7a-2;ID=MI0000836

Chr1  miRBase     miRNA 135254133   135254222   .     +     .     Name=rno-mir-9-3;ID=MI0000839

Chr1  miRBase     miRNA 153476669   153476756   .     +     .     Name=rno-mir-708;ID=MI0006160

 

 

But when I load the volvox data with :

 

ctgA  example     contig      1     50000 .     .     .     Name=ctgA

ctgA  example     remark      1659  1984  .     +     .     Name=f07;Note=This is an example

ctgA  example     remark      3014  6130  .     +     .     Name=f06;Note=This is another example

ctgA  example     remark      4715  5968  .     -     .     Name=f05;Note=Ok! Ok! I get the message.

ctgA  example     remark      13280 16394 .     +     .     Name=f08

ctgA  example     remark      15329 15533 .     +     .     Name=f10

ctgA  example     remark      19157 22915 .     -     .     Name=f13

ctgA  example     remark      22132 24633 .     +     .     Name=f15

ctgA  example     remark      23072 23185 .     +     .     Name=f14

ctgA  example     remark      24562 28338 .     +     .     Name=f02

ctgA  example     remark      36034 38167 .     +     .     Name=f09

ctgA  example     remark      36649 40440 .     -     .     Name=f03

ctgA  example     remark      37242 38653 .     +     .     Name=f04

ctgA  example     remark      44705 47713 .     -     .     Name=f01

ctgA  example     remark      46990 48410 .     -     .     Name=f11

ctgA  example     remark      49758 50000 .     -     .     Name=f12

 

 

It doesn’t seem to have a problem..

I have loaded the same miRNA gff3 files a month ago on my CENTOS Virtual box and it seemed to accept it fine..

 

What must I change in the gff3 files?

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Ram Podicheti [mailto:[hidden email]]
Sent: Wednesday, May 26, 2010 6:31 AM
To: Scott Cain
Cc: [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Scott, that makes a whole lot sense - Name is required for that landmark to be found.

Thanks,

 

Ram

On Tue, May 25, 2010 at 10:54 PM, Scott Cain <[hidden email]> wrote:

Hi Ram,

Name is used for what you would call a feature; that is, what you would search for if you were looking for that feature, so you should definitely have Name=chr1.  ID is a little more fuzzy; while it shouldn't be required, in older releases of Bio::DB::SeqFeature::Store, I think there may have been times when it was required, but according to the spec, it shouldn't be.

Scott



On Tue, May 25, 2010 at 8:37 PM, Ram Podicheti <[hidden email]> wrote:

Is it normal for GBrowse to expect both ID and Name attributes for SeqID? Most of the standard gff datasets, including those from NCBI, that I have noticed make sure that both the attributes are included. Is Name not meant for supplying a visual element in the form of label alone?

Thanks,

 

Ram

On Tue, May 25, 2010 at 8:27 PM, Lincoln Stein <[hidden email]> wrote:

This is the expected behavior when you are not viewing a region.

 

Lincoln

 

On Tue, May 25, 2010 at 3:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

Error! Filename not specified.

 

 

 

But when I chose the test data source I get this:

Error! Filename not specified.

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


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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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------------------------------------------------------------------------
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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help with conf file - resolved - well.. almost

Jayaraman, Pushkala
In reply to this post by Ram Podicheti

Hello,

This is how I resolved the issue with my gbrowse2 not displaying any of the panels

 

I dumped the mysql database that I had created on my VirtualBox (out of the same input data that I am using on the server) and I copied that database dump onto the database on the server and it worked..

I was able to see all the glyphs.. and all the tracks..

 

My Solaris server has the mysql version :

mysql  Ver 14.12 Distrib 5.0.45, for sun-solaris2.10 (sparc) using  EditLine wrapper

 

whereas my VirtualBox has the mysql version:

mysql  Ver 14.12 Distrib 5.0.77, for redhat-linux-gnu (i686) using readline 5.1

 

When I try to use the bp_seqfeature_load.pl with the –f option on the cmd line on my red hat Linux on the VirtualBox, It seems to work really well with no errors.. but when I try to load the same data using the bp_seqfeature_load.pl with the –f option on the Solaris server it gives me this Stack Trace error:

Building object tree... 0.00s                                                                              

Loading bulk data into database...DBD::mysql::db do failed: The used command is not allowed with this MySQL version at /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 544, <GEN0> line 26.

 

-------------------- EXCEPTION --------------------

MSG: The used command is not allowed with this MySQL version

STACK Bio::DB::SeqFeature::Store::DBI::mysql::_finish_bulk_update /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm:544

STACK Bio::DB::SeqFeature::Store::finish_bulk_update /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:1467

STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:325

STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:325

STACK Bio::DB::SeqFeature::Store::Loader::load /usr/local/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:222

STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:112

 

Scott gave me the additional argument of mysql_local_infile=1 to be added to the dsn line..

 

Although adding this argument does not produce the error.. it does load the data onto the database but the web page or the conf file are not able to extract any data from the database to display on the track.. as you can see here: the miRnas are shown but the siRnas aren’t.. the miRnas and siRans are the same data with the exact start and stop positions except for changed attribute tags..

i.e rno-mir-99b in miRna is rno-mir-99b00 in siRna

But the siRna track isn’t visible at all..

Why does this problem occur? The Bioperl versions are the same on both places..

 

 

 

 

I also tried another debugging method: I created a database on the solaris server using the bp_seqfeature_load.pl there and then tried to access that database from my Virtualbox. The result: the Gbrowse Overview/region and detail panels on the Virtual Box disappeared…. The exact same behavior that was being shown by the gbrowse on solaris..

 

Has anyone had a similar problem??? How do I rectify it?

For now I am temporarily creating the entire database on my VirtualBox and then creating a database dump and porting it over to the server side so that my DBA can upload it..(which is twice the amount of work that one would normally do for gbrowse data creation)

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 7:37 PM
To: Lincoln Stein
Cc: Jayaraman, Pushkala; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Is it normal for GBrowse to expect both ID and Name attributes for SeqID? Most of the standard gff datasets, including those from NCBI, that I have noticed make sure that both the attributes are included. Is Name not meant for supplying a visual element in the form of label alone?

Thanks,

 

Ram

On Tue, May 25, 2010 at 8:27 PM, Lincoln Stein <[hidden email]> wrote:

This is the expected behavior when you are not viewing a region.

 

Lincoln

 

On Tue, May 25, 2010 at 3:32 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think I found the missing piece:

When I viewed the page source and debugged using the firefox debugger I found that:

Somehow mysteriously the HTML section after “plugin_configure_div” until <div_id=”tracks_panel_show” seems to disappear. I did view source on firefox and debugged line by line..

Any reason why this section should disappear?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:19 PM
To: Ram Podicheti
Cc: [hidden email]; Gbrowse Mailing List


Subject: Re: [Gmod-gbrowse] help with conf file

 

Thanks Ram,

I think that is one of the errors but an even crazier error is this:

When I check the yeast data source, I get the whole page as is:

 

 

 

But when I chose the test data source I get this:

 

 

This is what is the most weird...

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Tuesday, May 25, 2010 4:12 PM
To: Jayaraman, Pushkala
Cc: Scott Cain; [hidden email]; Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] help with conf file

 

Pushkala,

I am not sure how pertinent my message would be to your problem, but I

noticed something weird in the way GBrowse handles certain GFF3 files.

At times, in the GFF3 file, GBrowse expects a 'Name' attribute besides

the 'ID' in the line representing the reference sequence.

 

Chr1    MySource   chromosome   1   12345678   .   +   .   ID=Chr1;Name=Chr1

 

If the Name is omitted, you may get the 'landmark not recognized' error.

Please note that this is not always the case, hence I called it 'weird'.

Moreover, I thought 'Name' is meant to provide only a label and not

required by GBrowse to identify the seqid.

 

So, try giving a Name besides the ID and see how that goes.

Cheers,

 

Ram

 

 

Jayaraman, Pushkala wrote:

> I'm trying to load the database by removing the -f feature.. I will

> add the local parameter and check.. I did read about it in the forums

> but did not think it necessary for my database as I never added it for

> the database on localhost.

> Although, even with SeqFeature Store, I do not see the overview region

> or the details panel

> Herewith is attached a picture: If you see the picture on the right

> screen, You will notice that there is no scale..

> How do it rectify this?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> -----Original Message-----

> From: Scott Cain [mailto:[hidden email]]

> Sent: Tuesday, May 25, 2010 3:30 PM

> To: Jayaraman, Pushkala

> Cc: Gbrowse Mailing List; [hidden email]

> Subject: Re: [Gmod-gbrowse] help with conf file

> If you remove the callback does it go back to working?

> Scott

> On Tue, May 25, 2010 at 3:16 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> > Nope! The error log seems to run as though nothing happened..

> >

> >

> > Pushkala Jayaraman

> > Programmer/Analyst

> > Rat Genome Database

> > Human and Molecular Genetics Center

> > Medical College of Wisconsin

> > Email: [hidden email]

> > Work: 414-955-2229

> > www.rgd.mcw.edu

> >

> >

> > -----Original Message-----

> > From: Scott Cain [mailto:[hidden email]]

> > Sent: Tuesday, May 25, 2010 1:35 PM

> > To: Jayaraman, Pushkala

> > Cc: Gbrowse Mailing List; [hidden email]

> > Subject: Re: [Gmod-gbrowse] help with conf file

> >

> > Hi Pushkala,

> >

> > Are there any messages in the error log?

> >

> > Scott

> >

> >

> >

> >

> > On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala

> <[hidden email]> wrote:

> >> Hello after resolving issues with database access, I see that I get

> this

> >> when I try accessing gborwse2

> >>

> >>

> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2

> >>

> >>

> >>

> >> I am not able to see the overview/region/detail panels..

> >>

> >>

> >>

> >> I know there is something wrong with the config file.. but I am

> just not

> >> sure what..

> >>

> >>

> >>

> >> Herewith is my config file:

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> [GENERAL]

> >>

> >> description   = Rat Genome V3.4 Assembly

> >>

> >> db_adaptor    = Bio::DB::GFF

> >>

> >> db_args       = -adaptor dbi::mysql

> >>

> >>                 -dsn

> >> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306

> >>

> >>                                 -user rgdselect

> >>

> >>                                 -pass rgdselusrdv1a

> >>

> >>

> >>

> >> # examples to show in the introduction

> >>

> >> examples = proteinuria

> >>

> >>            Grik1

> >>

> >>            RGD620956

> >>

> >>

> >>

> >> # Default track settings

> >>

> >> [TRACK DEFAULTS]

> >>

> >> glyph       = generic

> >>

> >> height      = 8

> >>

> >> bgcolor     = cyan

> >>

> >> fgcolor     = cyan

> >>

> >> font2color  = black

> >>

> >> label density = 25

> >>

> >>

> >>

> >> ### Individual track settings ####

> >>

> >> [PSEUDOGENE:overview]

> >>

> >> category     = GENE MODELS

> >>

> >> feature      = pseudogene:GenBank

> >>

> >> glyph        = arrow

> >>

> >> fgcolor      = blue

> >>

> >> linewidth    = 2

> >>

> >> height       = 6

> >>

> >> link   = sub {

> >>

> >>                   my $f=shift;

> >>

> >>                   if ($f->attributes->{'Dbxref'} eq "") {

> >>

> >>                       return;

> >>

> >>                   }

> >>

> >>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});

> >>

> >>                   my $ncbiId;

> >>

> >>                   if ($xdb =~/GeneID:(\d+)/) {

> >>

> >>                     $ncbiId=$1;

> >>

> >>                   }

> >>

> >>                   return

> >>

> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";

> >>

> >>                 }

> >>

> >> key          =  Entrez Pseudogenes

> >>

> >> citation     = This track shows pseudogenes labeled as such at <a

> >> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering

> over a

> >> feature provides additional annotation including the EntrezGeneID,

> Name,

> >> Description, and Source. Clicking on a features links to the

> appropriate

> >> EntrezGene record.

> >>

> >>

> >>

> >>

> >>

> >>

> >>

> >> I know there is absolutely nothing here..

> >>

> >> But I am just not able to see the Overview/Region/detail panels or the

> >> glyphs.. I can see the section that allows you to search for

> keywords/click

> >> on what tracks you need ON/select datasource.

> >>

> >> I can even see the Overview/Region/Detail sections when I chose

> some of the

> >> sample datasets provided eg Yeast Basic and yeast Advanced..

> >>

> >>

> >>

> >> Where am I going wrong?

> >>

> >>

> >>

> >> Pushkala Jayaraman

> >>

> >> Programmer/Analyst

> >>

> >> Rat Genome Database

> >>

> >> Human and Molecular Genetics Center

> >>

> >> Medical College of Wisconsin

> >>

> >> Email: [hidden email]

> >>

> >> Work: 414-955-2229

> >>

> >> www.rgd.mcw.edu

> >>

> >>

> >>

> >>

> ------------------------------------------------------------------------------

> >>

> >>

> >> _______________________________________________

> >> Gmod-gbrowse mailing list

> >> [hidden email]

> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> >>

> >>

> >

> >

> >

> > --

> > ------------------------------------------------------------------------

> > Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> > GMOD Coordinator (http://gmod.org/)                     216-392-3087

> > Ontario Institute for Cancer Research

> >

> --

> ------------------------------------------------------------------------

> Scott Cain, Ph. D.                                   scott at

> scottcain dot net

> GMOD Coordinator (http://gmod.org/)                     216-392-3087

> Ontario Institute for Cancer Research

> ------------------------------------------------------------------------

> ------------------------------------------------------------------------------

>  

> ------------------------------------------------------------------------

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


------------------------------------------------------------------------------


_______________________________________________
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[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]>

 


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