sphuang | 1 May 06:21 2011
Picon

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.

------------------------------------------------------------------------------
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
Scott Cain | 2 May 01:30 2011
Picon

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

------------------------------------------------------------------------------
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
manju rawat | 2 May 06:23 2011
Picon

Re: gff3 file creation

I have raw sequence???i jsut want to learn how to create gff3 file from any sequence to upload in gbrowse..

------------------------------------------------------------------------------
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
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Dan Bolser | 2 May 11:14 2011
Picon

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.

------------------------------------------------------------------------------
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
Emmanuel Quevillon | 2 May 11:26 2011
Picon
Picon

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

------------------------------------------------------------------------------
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
Peter Cock | 2 May 12:07 2011

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

------------------------------------------------------------------------------
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
Barris, Wes | 2 May 15:54 2011

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.
> 
> -----------------------------------------------------------------------
> ------- 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
> _______________________________________________ Gmod-gbrowse mailing
> list Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

-- 
Wes Barris

This email and any files transmitted with it are confidential and intended solely for the use of the
addressee. If you are not the intended addressee, then you have received this email in error and any use,
dissemination, forwarding, printing, or copying of this email is strictly prohibited. Please notify us
immediately of your unintended receipt by reply and then delete this email and your reply.
Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be held liable to any person resulting
from the unintended or unauthorized use of any information contained in this email or as a result of any
additions or deletions of information originally contained in this email.

------------------------------------------------------------------------------
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
Duke | 2 May 16:29 2011
Picon

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.

------------------------------------------------------------------------------
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
Scott Cain | 2 May 18:14 2011
Picon

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
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> 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

------------------------------------------------------------------------------
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
Scott Cain | 2 May 18:15 2011
Picon

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.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> 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

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

Gmane