more recent flybase.gff conf file

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more recent flybase.gff conf file

Georg Vogler
Hi!

I've successfully setup GBrowse2 with the current flybase release on a local Ubuntu server (phew). I now want to display the tracks and features, but the default or WebGBrowse generated .conf files fail to generate nice tracks. I'm now using a fly.gff3.conf (found here: http://www.geboc.org/gbrowse/contrib/conf_files/09.fly.gff3.conf) and the data is displayed much nicer. I was wondering if there is a more recent version of that file available, and also if there is a manual/documentation available to understand and tweak that file.

Many thanks in advance,

Geo

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Re: more recent flybase.gff conf file

Scott Cain
Hi Geo,

I don't have a more recent fly configuration, and I imagine the one
that ships with GBrowse is quite old.  There is quite a bit of
documentation for working with GBrowse configurations.  The best place
to start is the GBrowse tutorial, which also comes with GBrowse:

  http://www.geboc.org/gbrowse/tutorial/tutorial.html

(Though I'd point out that this instance of GBrowse is pretty old; you
might want to look at getting GBrowse2).  Also, there is a fairly long
configuration document on the GMOD wiki:

  http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO

Which is the document for working with GBrowse1 configuration files
(which you have).  Virtually everything in this document for
configuring tracks applies to GBrowse2 as well, though there are new
options for GBrowse2.

Scott


On Fri, Oct 26, 2012 at 3:06 PM, Georg Vogler
<[hidden email]> wrote:

> Hi!
>
> I've successfully setup GBrowse2 with the current flybase release on a local
> Ubuntu server (phew). I now want to display the tracks and features, but the
> default or WebGBrowse generated .conf files fail to generate nice tracks.
> I'm now using a fly.gff3.conf (found here:
> http://www.geboc.org/gbrowse/contrib/conf_files/09.fly.gff3.conf) and the
> data is displayed much nicer. I was wondering if there is a more recent
> version of that file available, and also if there is a manual/documentation
> available to understand and tweak that file.
>
> Many thanks in advance,
>
> Geo
>
> ------------------------------------------------------------------------------
> WINDOWS 8 is here.
> Millions of people.  Your app in 30 days.
> Visit The Windows 8 Center at Sourceforge for all your go to resources.
> http://windows8center.sourceforge.net/
> join-generation-app-and-make-money-coding-fast/
> _______________________________________________
> 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: more recent flybase.gff conf file

Georg Vogler
Hi, Scott!

You are absolutely right. I've been playing with the fly.conf config file
and have my site up and running, with the only 'outdated' part being the
link sections to Flybase.

Here is the original section, and it was/is tricky to extract the correct
tag_values from the database. I could get it to work with try and error,
but haven't really understood what this piece of code exactly does (I
barely know Perl). If you (or someone) can provide some insight here I
would really appreciate that a lot.

link = sub {
  my $f= shift;
  my $d=
join(',',$f->each_tag_value(''),$f->id(),$f->each_tag_value('Alias'));
  my $tp= $f->class;
  my $best='(FB\w\w\d+)';
  if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
  elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; }
  elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; }
  elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; }
  elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; }
  if ($d =~ /$best/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
  elsif ($d =~ /(FB\w\w\d+)/){ return
'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
  elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return
'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
  if ($f->name()) { return
'http://flybase.org/cgi-bin/fbsymq.html?'.$f->name(); }
  }



Best,

Geo







Am 11/7/12 11:29 AM schrieb "Scott Cain" unter <[hidden email]>:

>Hi Geo,
>
>I don't have a more recent fly configuration, and I imagine the one
>that ships with GBrowse is quite old.  There is quite a bit of
>documentation for working with GBrowse configurations.  The best place
>to start is the GBrowse tutorial, which also comes with GBrowse:
>
>  http://www.geboc.org/gbrowse/tutorial/tutorial.html
>
>(Though I'd point out that this instance of GBrowse is pretty old; you
>might want to look at getting GBrowse2).  Also, there is a fairly long
>configuration document on the GMOD wiki:
>
>  http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO
>
>Which is the document for working with GBrowse1 configuration files
>(which you have).  Virtually everything in this document for
>configuring tracks applies to GBrowse2 as well, though there are new
>options for GBrowse2.
>
>Scott
>
>
>On Fri, Oct 26, 2012 at 3:06 PM, Georg Vogler
><[hidden email]> wrote:
>> Hi!
>>
>> I've successfully setup GBrowse2 with the current flybase release on a
>>local
>> Ubuntu server (phew). I now want to display the tracks and features,
>>but the
>> default or WebGBrowse generated .conf files fail to generate nice
>>tracks.
>> I'm now using a fly.gff3.conf (found here:
>> http://www.geboc.org/gbrowse/contrib/conf_files/09.fly.gff3.conf) and
>>the
>> data is displayed much nicer. I was wondering if there is a more recent
>> version of that file available, and also if there is a
>>manual/documentation
>> available to understand and tweak that file.
>>
>> Many thanks in advance,
>>
>> Geo
>>
>>
>>-------------------------------------------------------------------------
>>-----
>> WINDOWS 8 is here.
>> Millions of people.  Your app in 30 days.
>> Visit The Windows 8 Center at Sourceforge for all your go to resources.
>> http://windows8center.sourceforge.net/
>> join-generation-app-and-make-money-coding-fast/
>> _______________________________________________
>> 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: more recent flybase.gff conf file

Scott Cain
Hi Geo,

I understand perl well enough, but I don't really know how to write
URLs into FlyBase.  Perhaps asking for technical assistance from the
FlyBase folks would be a good thing to do.  They are pretty good about
answering questions like this.

Scott


On Wed, Nov 7, 2012 at 3:10 PM, Georg Vogler <[hidden email]> wrote:

> Hi, Scott!
>
> You are absolutely right. I've been playing with the fly.conf config file
> and have my site up and running, with the only 'outdated' part being the
> link sections to Flybase.
>
> Here is the original section, and it was/is tricky to extract the correct
> tag_values from the database. I could get it to work with try and error,
> but haven't really understood what this piece of code exactly does (I
> barely know Perl). If you (or someone) can provide some insight here I
> would really appreciate that a lot.
>
> link = sub {
>   my $f= shift;
>   my $d=
> join(',',$f->each_tag_value(''),$f->id(),$f->each_tag_value('Alias'));
>   my $tp= $f->class;
>   my $best='(FB\w\w\d+)';
>   if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
>   elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; }
>   elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; }
>   elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; }
>   elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; }
>   if ($d =~ /$best/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>   elsif ($d =~ /(FB\w\w\d+)/){ return
> 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>   elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return
> 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>   if ($f->name()) { return
> 'http://flybase.org/cgi-bin/fbsymq.html?'.$f->name(); }
>   }
>
>
>
> Best,
>
> Geo
>
>
>
>
>
>
>
> Am 11/7/12 11:29 AM schrieb "Scott Cain" unter <[hidden email]>:
>
>>Hi Geo,
>>
>>I don't have a more recent fly configuration, and I imagine the one
>>that ships with GBrowse is quite old.  There is quite a bit of
>>documentation for working with GBrowse configurations.  The best place
>>to start is the GBrowse tutorial, which also comes with GBrowse:
>>
>>  http://www.geboc.org/gbrowse/tutorial/tutorial.html
>>
>>(Though I'd point out that this instance of GBrowse is pretty old; you
>>might want to look at getting GBrowse2).  Also, there is a fairly long
>>configuration document on the GMOD wiki:
>>
>>  http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO
>>
>>Which is the document for working with GBrowse1 configuration files
>>(which you have).  Virtually everything in this document for
>>configuring tracks applies to GBrowse2 as well, though there are new
>>options for GBrowse2.
>>
>>Scott
>>
>>
>>On Fri, Oct 26, 2012 at 3:06 PM, Georg Vogler
>><[hidden email]> wrote:
>>> Hi!
>>>
>>> I've successfully setup GBrowse2 with the current flybase release on a
>>>local
>>> Ubuntu server (phew). I now want to display the tracks and features,
>>>but the
>>> default or WebGBrowse generated .conf files fail to generate nice
>>>tracks.
>>> I'm now using a fly.gff3.conf (found here:
>>> http://www.geboc.org/gbrowse/contrib/conf_files/09.fly.gff3.conf) and
>>>the
>>> data is displayed much nicer. I was wondering if there is a more recent
>>> version of that file available, and also if there is a
>>>manual/documentation
>>> available to understand and tweak that file.
>>>
>>> Many thanks in advance,
>>>
>>> Geo
>>>
>>>
>>>-------------------------------------------------------------------------
>>>-----
>>> WINDOWS 8 is here.
>>> Millions of people.  Your app in 30 days.
>>> Visit The Windows 8 Center at Sourceforge for all your go to resources.
>>> http://windows8center.sourceforge.net/
>>> join-generation-app-and-make-money-coding-fast/
>>> _______________________________________________
>>> 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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Automate, monitor and manage. Do more in less time with Central
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Re: more recent flybase.gff conf file

girlwithglasses
Hello Georg,

I would imagine that you figured out that the piece of code is looking
at the class of object that you're dealing with (gene, transposable
element, etc.) and trying to generate an appropriate identifier from
that information. FlyBase did update their generic URLs for accessing
database objects a little while ago; the syntax they use now is
http://flybase.org/reports/[example_id].html, e.g.
http://flybase.org/reports/FBgn0000024.html . To update your config
file, you'd substitute

'http://flybase.org/cgi-bin/fbidq.html?'.$1

with

'http://flybase.org/reports/' . $1 . '.html'

( source: http://www.geneontology.org/cgi-bin/xrefs.cgi#ref-f )

You could see if that fixes your issue; otherwise, as Scott says, the
best thing is to contact FlyBase directly for assistance.

Best of luck!
Amelia.

On Wed, Nov 7, 2012 at 12:36 PM, Scott Cain <[hidden email]> wrote:

> Hi Geo,
>
> I understand perl well enough, but I don't really know how to write
> URLs into FlyBase.  Perhaps asking for technical assistance from the
> FlyBase folks would be a good thing to do.  They are pretty good about
> answering questions like this.
>
> Scott
>
>
> On Wed, Nov 7, 2012 at 3:10 PM, Georg Vogler <[hidden email]> wrote:
>> Hi, Scott!
>>
>> You are absolutely right. I've been playing with the fly.conf config file
>> and have my site up and running, with the only 'outdated' part being the
>> link sections to Flybase.
>>
>> Here is the original section, and it was/is tricky to extract the correct
>> tag_values from the database. I could get it to work with try and error,
>> but haven't really understood what this piece of code exactly does (I
>> barely know Perl). If you (or someone) can provide some insight here I
>> would really appreciate that a lot.
>>
>> link = sub {
>>   my $f= shift;
>>   my $d=
>> join(',',$f->each_tag_value(''),$f->id(),$f->each_tag_value('Alias'));
>>   my $tp= $f->class;
>>   my $best='(FB\w\w\d+)';
>>   if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
>>   elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; }
>>   elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; }
>>   elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; }
>>   elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; }
>>   if ($d =~ /$best/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>>   elsif ($d =~ /(FB\w\w\d+)/){ return
>> 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>>   elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return
>> 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>>   if ($f->name()) { return
>> 'http://flybase.org/cgi-bin/fbsymq.html?'.$f->name(); }
>>   }
>>
>>
>>
>> Best,
>>
>> Geo
>>
>>
>>
>>
>>
>>
>>
>> Am 11/7/12 11:29 AM schrieb "Scott Cain" unter <[hidden email]>:
>>
>>>Hi Geo,
>>>
>>>I don't have a more recent fly configuration, and I imagine the one
>>>that ships with GBrowse is quite old.  There is quite a bit of
>>>documentation for working with GBrowse configurations.  The best place
>>>to start is the GBrowse tutorial, which also comes with GBrowse:
>>>
>>>  http://www.geboc.org/gbrowse/tutorial/tutorial.html
>>>
>>>(Though I'd point out that this instance of GBrowse is pretty old; you
>>>might want to look at getting GBrowse2).  Also, there is a fairly long
>>>configuration document on the GMOD wiki:
>>>
>>>  http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO
>>>
>>>Which is the document for working with GBrowse1 configuration files
>>>(which you have).  Virtually everything in this document for
>>>configuring tracks applies to GBrowse2 as well, though there are new
>>>options for GBrowse2.
>>>
>>>Scott
>>>
>>>
>>>On Fri, Oct 26, 2012 at 3:06 PM, Georg Vogler
>>><[hidden email]> wrote:
>>>> Hi!
>>>>
>>>> I've successfully setup GBrowse2 with the current flybase release on a
>>>>local
>>>> Ubuntu server (phew). I now want to display the tracks and features,
>>>>but the
>>>> default or WebGBrowse generated .conf files fail to generate nice
>>>>tracks.
>>>> I'm now using a fly.gff3.conf (found here:
>>>> http://www.geboc.org/gbrowse/contrib/conf_files/09.fly.gff3.conf) and
>>>>the
>>>> data is displayed much nicer. I was wondering if there is a more recent
>>>> version of that file available, and also if there is a
>>>>manual/documentation
>>>> available to understand and tweak that file.
>>>>
>>>> Many thanks in advance,
>>>>
>>>> Geo
>>>>
>>>>
>>>>-------------------------------------------------------------------------
>>>>-----
>>>> WINDOWS 8 is here.
>>>> Millions of people.  Your app in 30 days.
>>>> Visit The Windows 8 Center at Sourceforge for all your go to resources.
>>>> http://windows8center.sourceforge.net/
>>>> join-generation-app-and-make-money-coding-fast/
>>>> _______________________________________________
>>>> 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
>
> ------------------------------------------------------------------------------
> LogMeIn Central: Instant, anywhere, Remote PC access and management.
> Stay in control, update software, and manage PCs from one command center
> Diagnose problems and improve visibility into emerging IT issues
> Automate, monitor and manage. Do more in less time with Central
> http://p.sf.net/sfu/logmein12331_d2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Amelia Ireland
GMOD Community Support || http://gmod.org

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Re: more recent flybase.gff conf file

Georg Vogler
Hi!

Thanks for your advice. Below is the reply I got from FlyBase, with some
more basic URLs. I will rework the links and post the working config file
once it works for all data types.

Best,

Geo



>>Hi Geo,
>>
>>Here is how I would change this without knowing more about the context
>>of this code snippet.
>>
link = sub {
  my $f= shift;
  my $d=
join(',',$f->each_tag_value(''),$f->id(),$f->each_tag_value('Alias'));
  my $tp= $f->class;
  my $best='(FB\w\w\d+)';
  if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
  elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; }
  elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; }
  elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; }
  elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; }
  if ($d =~ /$best/){ return 'http://flybase.org/reports/'.$1; }
  elsif ($d =~ /(FB\w\w\d+)/){ return
'http://flybase.org/reports/'.$1; }
  elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return
'http://flybase.org/search/simple/symbol/'.$1; }
  if ($f->name()) { return
'http://flybase.org/search/simple/symbol/'.$f->name(); }
  }

Here are some basic URLs that we offer for linking:
http://flybase.org/reports/<FBID>  - Direct link to report
http://flybase.org/search/simple/<FB DATA CLASS>/<TERM> - Full text search
within the specified data class.
http://flybase.org/search/simple/symbol/<TERM>  - Symbol search across all
data classes.
http://flybase.org/search/simple/<TERM> - Full text search across all data
classes.

<FBID> - the FlyBase ID of the object (e.g. FBgn0001234)
<FB DATA CLASS> - The FlyBase data class namespace (e.g. FBgn, FBtr, FBpp,
FBal, FBti, etc.)
<TERM> - Your search term.

http://flybase.org/reports/FBgn0000490
http://flybase.org/search/simple/FBgn/embryonic%20stage%2011
http://flybase.org/search/simple/symbol/cnn
http://flybase.org/search/simple/IPR000375


>>Cheers,
>>Josh





Am 11/7/12 2:22 PM schrieb "Amelia Ireland" unter
<[hidden email]>:

>Hello Georg,
>
>I would imagine that you figured out that the piece of code is looking
>at the class of object that you're dealing with (gene, transposable
>element, etc.) and trying to generate an appropriate identifier from
>that information. FlyBase did update their generic URLs for accessing
>database objects a little while ago; the syntax they use now is
>http://flybase.org/reports/[example_id].html, e.g.
>http://flybase.org/reports/FBgn0000024.html . To update your config
>file, you'd substitute
>
>'http://flybase.org/cgi-bin/fbidq.html?'.$1
>
>with
>
>'http://flybase.org/reports/' . $1 . '.html'
>
>( source: http://www.geneontology.org/cgi-bin/xrefs.cgi#ref-f )
>
>You could see if that fixes your issue; otherwise, as Scott says, the
>best thing is to contact FlyBase directly for assistance.
>
>Best of luck!
>Amelia.
>
>On Wed, Nov 7, 2012 at 12:36 PM, Scott Cain <[hidden email]> wrote:
>> Hi Geo,
>>
>> I understand perl well enough, but I don't really know how to write
>> URLs into FlyBase.  Perhaps asking for technical assistance from the
>> FlyBase folks would be a good thing to do.  They are pretty good about
>> answering questions like this.
>>
>> Scott
>>
>>
>> On Wed, Nov 7, 2012 at 3:10 PM, Georg Vogler
>><[hidden email]> wrote:
>>> Hi, Scott!
>>>
>>> You are absolutely right. I've been playing with the fly.conf config
>>>file
>>> and have my site up and running, with the only 'outdated' part being
>>>the
>>> link sections to Flybase.
>>>
>>> Here is the original section, and it was/is tricky to extract the
>>>correct
>>> tag_values from the database. I could get it to work with try and
>>>error,
>>> but haven't really understood what this piece of code exactly does (I
>>> barely know Perl). If you (or someone) can provide some insight here I
>>> would really appreciate that a lot.
>>>
>>> link = sub {
>>>   my $f= shift;
>>>   my $d=
>>> join(',',$f->each_tag_value(''),$f->id(),$f->each_tag_value('Alias'));
>>>   my $tp= $f->class;
>>>   my $best='(FB\w\w\d+)';
>>>   if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
>>>   elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; }
>>>   elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; }
>>>   elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; }
>>>   elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; }
>>>   if ($d =~ /$best/){ return
>>>'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>>>   elsif ($d =~ /(FB\w\w\d+)/){ return
>>> 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>>>   elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return
>>> 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
>>>   if ($f->name()) { return
>>> 'http://flybase.org/cgi-bin/fbsymq.html?'.$f->name(); }
>>>   }
>>>
>>>
>>>
>>> Best,
>>>
>>> Geo
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Am 11/7/12 11:29 AM schrieb "Scott Cain" unter <[hidden email]>:
>>>
>>>>Hi Geo,
>>>>
>>>>I don't have a more recent fly configuration, and I imagine the one
>>>>that ships with GBrowse is quite old.  There is quite a bit of
>>>>documentation for working with GBrowse configurations.  The best place
>>>>to start is the GBrowse tutorial, which also comes with GBrowse:
>>>>
>>>>  http://www.geboc.org/gbrowse/tutorial/tutorial.html
>>>>
>>>>(Though I'd point out that this instance of GBrowse is pretty old; you
>>>>might want to look at getting GBrowse2).  Also, there is a fairly long
>>>>configuration document on the GMOD wiki:
>>>>
>>>>  http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO
>>>>
>>>>Which is the document for working with GBrowse1 configuration files
>>>>(which you have).  Virtually everything in this document for
>>>>configuring tracks applies to GBrowse2 as well, though there are new
>>>>options for GBrowse2.
>>>>
>>>>Scott
>>>>
>>>>
>>>>On Fri, Oct 26, 2012 at 3:06 PM, Georg Vogler
>>>><[hidden email]> wrote:
>>>>> Hi!
>>>>>
>>>>> I've successfully setup GBrowse2 with the current flybase release on
>>>>>a
>>>>>local
>>>>> Ubuntu server (phew). I now want to display the tracks and features,
>>>>>but the
>>>>> default or WebGBrowse generated .conf files fail to generate nice
>>>>>tracks.
>>>>> I'm now using a fly.gff3.conf (found here:
>>>>> http://www.geboc.org/gbrowse/contrib/conf_files/09.fly.gff3.conf) and
>>>>>the
>>>>> data is displayed much nicer. I was wondering if there is a more
>>>>>recent
>>>>> version of that file available, and also if there is a
>>>>>manual/documentation
>>>>> available to understand and tweak that file.
>>>>>
>>>>> Many thanks in advance,
>>>>>
>>>>> Geo
>>>>>
>>>>>
>>>>>----------------------------------------------------------------------
>>>>>---
>>>>>-----
>>>>> WINDOWS 8 is here.
>>>>> Millions of people.  Your app in 30 days.
>>>>> Visit The Windows 8 Center at Sourceforge for all your go to
>>>>>resources.
>>>>> http://windows8center.sourceforge.net/
>>>>> join-generation-app-and-make-money-coding-fast/
>>>>> _______________________________________________
>>>>> 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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>
>
>
>--
>Amelia Ireland
>GMOD Community Support || http://gmod.org


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