Re: Disappearing Balloons in GB 2.26, IE8

I have the same problem when using Gbrowse 2.28 and IE8. And I got the idea
of fixing it from the following post:
http://generic-model-organism-system-database.450254.n5.nabble.com/GBox-doiesnt-fire-in-Internet-Explorer-td2852920.html

Generally, you need to make a minor change in the file "RenderPanels.pm". 
In the file around Line 1233, you need to add the text in bold.
    my %attributes = (
                      title       => $title,
                      href        => $href,
                      target      => $target,
                      onmouseover => $mouseover,
                      onmousedown => $mousedown.";return false;",   
                      style       => $style,
                      );

This will make the balloons appear in IE8.--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Disappearing-Balloons-in-GB-2-26-IE8-tp4282235p4362304.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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Re: gff3 file creation

Hi Manju,

When you say you have sequence, what do you mean?  You have raw sequence from a sequencer, you have an assembly
somebody gave you, you have genbank files, or something else?

Scott

Sent from my iPad

On 2011-04-30, at 7:26 AM, manju rawat <manju.rawat2@...> wrote:

> 
> Hello Sir,
> 
> How to create gff3 files for the gbrowse???
> I have  sequence...and i dont know how to create gff3??
> If anyboy konw any site aur any software by which we can crete gff3 file pls tell  me....
> 
> 
> Thanks
> Manju Rawat

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Re: gff3 file creation

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Feature vs. Landmark?

Hi,

When a feature and a landmark share the same ID, how do you select one
or the other in GBrowse?

Cheers,
Dan.

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2 reference genomes

Hi all,

I am in the charge of displaying genomic annotations using GBrowse.
Until now it as been quite simple with tools provided by BioPerl and 
GMOD to do so.
However, I had a new request for displaying annotations :

It is possible to have more than one reference genome or chromosome 
in GBrowse? The idea is to be able to compare 2 annotations made one 
2 different bacterial strains.
Does anybody knows if it is possible using GBrowse? If so, can 
someone guide me to the process to do it?

Thanks for any reply.

Regards
--

-- 
-------------------------
Emmanuel Quevillon
Projects and Development in Bioinformatics [PDB]
Institut Pasteur
+33 1 44 38 95 98
tuco at_ pasteur dot fr
-------------------------

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Re: gff3 file creation

On Mon, May 2, 2011 at 5:23 AM, manju rawat <manju.rawat2@...> wrote:
> I have raw sequence???i jsut want to learn how to create gff3 file from any
> sequence to upload in gbrowse..
>

Normally the GFF3 file will contain annotation (e.g. gene predictions) from
a tool like Glimmer or GeneMark.

However, you can construct a minimal GFF3 file which basically just lists
the DNA fragments.

I needed to do this for a draft genome where we don't yet have proper
annotations, but we did have transcriptome mapping data. I used the
following simple Python script (using Biopython) to create a minimal
GFF3 file from a FASTA file of our scaffolded contigs:

from Bio import SeqIO
handle = open("supercontigs.gff3", "w")
handle.write("##gff-version 3\n")
for record in SeqIO.parse("supercontigs.fasta", "fasta"):
    i = record.id
    l = len(record)
    handle.write("##sequence-region %s 1 %i\n" % (i, l))
    handle.write("%s\t.\tcontig\t1\t%i\t.\t.\t.\tID=%s\n" % (i, l, i))
    pass
handle.write("###\n")
handle.close()

Peter

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Re: Disappearing Balloons in GB 2.26, IE8

sphuang wrote on 2011-04-30:

> I have the same problem when using Gbrowse 2.28 and IE8. And I got the
> idea of fixing it from the following post:
> http://generic-model-organism-system-
> database.450254.n5.nabble.com/GBox-doiesnt-fire-in-Internet-Explorer-
> td2852920.html
> 
> Generally, you need to make a minor change in the file
> "RenderPanels.pm". In the file around Line 1233, you need to add the
> text in bold.
>     my %attributes = (
>                       title       => $title,
>                       href        => $href,
>                       target      => $target,
>                       onmouseover => $mouseover,
>                       onmousedown => $mousedown.";return false;",
>                       style       => $style,
>                       );

Hi Sphuang,

I am running IE8.0.7600.16385.  I tried applying your fix but it did not change the
behaviour.  When you click to display a popup balloon, the balloon appears for a
fraction of a second and then disappears.  I am using GBrowse-2.28.  What version of
IE8 are you running?

> This will make the balloons appear in IE8.-- View this message in
> context: http://generic-model-organism-system-
> database.450254.n5.nabble.com/Disappearing-Balloons-in-GB-2-26-IE8-
> tp4282235p4362304.html Sent from the gmod-gbrowse mailing list archive
> at Nabble.com.
> 
> -----------------------------------------------------------------------
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> _______________________________________________ Gmod-gbrowse mailing
> list Gmod-gbrowse@...
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mod_fcgid

Hi all,

My colleague tried to install GBrowse in a Red Hat server and he wanted 
to have fastCGI so he installed mod_fcgid and loaded the module. This 
server does not have mod_fastcgi by the way. But now he faced one issue: 
apache does not recognize fcgid directives:

$ service httpd start
 > Starting httpd: Syntax error on line 40 of 
/etc/httpd/conf.d/z_gbrowse2.conf:
 > Invalid command 'FcgidMinProcessesPerClass', perhaps misspelled or 
defined by a module not included in the server configuration
 >                                                             [FAILED]
 >

Any ideas why that error? Does he need mod_fastcgi together with mod_fcgid?

Thanks,

D.

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Re: 2 reference genomes

Hi Emmanuel,

It sounds like you want a synteny browser, right?  Perhaps you should
look at GBrowse_syn:

  http://gmod.org/wiki/Gbrowse_syn

Scott

On Mon, May 2, 2011 at 5:26 AM, Emmanuel Quevillon <tuco@...> wrote:
> Hi all,
>
> I am in the charge of displaying genomic annotations using GBrowse.
> Until now it as been quite simple with tools provided by BioPerl and
> GMOD to do so.
> However, I had a new request for displaying annotations :
>
> It is possible to have more than one reference genome or chromosome
> in GBrowse? The idea is to be able to compare 2 annotations made one
> 2 different bacterial strains.
> Does anybody knows if it is possible using GBrowse? If so, can
> someone guide me to the process to do it?
>
> Thanks for any reply.
>
> Regards
> --
> -------------------------
> Emmanuel Quevillon
> Projects and Development in Bioinformatics [PDB]
> Institut Pasteur
> +33 1 44 38 95 98
> tuco at_ pasteur dot fr
> -------------------------
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
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> Gmod-gbrowse mailing list
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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: Feature vs. Landmark?

Hi Dan,

Can you please flesh this question out a little more?  I'm not sure
what you're asking.

Scott

On Mon, May 2, 2011 at 5:14 AM, Dan Bolser <dan.bolser@...> wrote:
> Hi,
>
> When a feature and a landmark share the same ID, how do you select one
> or the other in GBrowse?
>
>
> Cheers,
> Dan.
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
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> Gmod-gbrowse mailing list
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>

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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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