Gbrowse_syn installation

[Wes Barris]

Hi,

I have followed the excellent Gbrowse_syn tutorial
http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
a working local copy of the sample rice/wild_rice synteny browser
working.  I have successfully completed all steps.  However, the
final gbrowse_syn/oryza display does not display the overview
or synteny display.  The following errors are displayed in the
apache error log:

[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine Bio::Graphics::Browser::Synteny::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm line 11
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at /htdocs/gbrowse/gbrowse_syn.cgi line 27
[Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element at
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm line 806.

Do the above errors mean anything to anywone?

I have upgraded Exporter to the latest version (5.63).
I am running the latest gbrowse from CVS (downloaded yesterday).
I am running bioperl 1.6.

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Hi Wes,

It looks like it might have something to to with the configuration
file.  Could you update your bioperl to a new svn checkout of bioperl-live
and also have you changed the configuration files at all?

Sheldon

On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...> wrote:

> Hi,
>
> I have followed the excellent Gbrowse_syn tutorial
> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
> a working local copy of the sample rice/wild_rice synteny browser
> working.  I have successfully completed all steps.  However, the
> final gbrowse_syn/oryza display does not display the overview
> or synteny display.  The following errors are displayed in the
> apache error log:
>
> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine Bio::Graphics::Browser::Synteny::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm line 11
> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at /htdocs/gbrowse/gbrowse_syn.cgi line 27
> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element at
> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm line 806.
>
> Do the above errors mean anything to anywone?
>
> I have upgraded Exporter to the latest version (5.63).
> I am running the latest gbrowse from CVS (downloaded yesterday).
> I am running bioperl 1.6.
>
> --
> Wes Barris <wes.barris@...>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Sheldon McKay wrote:
> Hi Wes,
>
> It looks like it might have something to to with the configuration
> file.  Could you update your bioperl to a new svn checkout of bioperl-live
> and also have you changed the configuration files at all?

Hi Sheldon,

I updated bioperl using the latest svn checkout.  This required me
to update several perl modules as well.  Now I'm completely
up-to-date.

I'm not seeing any difference in gbrowse_syn.  I'm getting these
errors in my apache error log file:

[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine Bio::Graphics::Browser::Synteny::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm line 11
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at /htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine Bio::Graphics::Browser::Synteny::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm line 11
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at /htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element at
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm line 806.

The only change that I have made to the three .conf files is to
change the -dsn args from "localhost" to the name of our database
server which runs mysql.

> Sheldon
>
> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...> wrote:
>> Hi,
>>
>> I have followed the excellent Gbrowse_syn tutorial
>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>> a working local copy of the sample rice/wild_rice synteny browser
>> working.  I have successfully completed all steps.  However, the
>> final gbrowse_syn/oryza display does not display the overview
>> or synteny display.  The following errors are displayed in the
>> apache error log:
>>
>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine Bio::Graphics::Browser::Synteny::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm line 11
>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at /htdocs/gbrowse/gbrowse_syn.cgi line 27
>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element at
>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm line 806.
>>
>> Do the above errors mean anything to anywone?
>>
>> I have upgraded Exporter to the latest version (5.63).
>> I am running the latest gbrowse from CVS (downloaded yesterday).
>> I am running bioperl 1.6.
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Hi Wes,

The shellwords error messages are not related, I think.  One more
question I forgot to ask: did you update Bio::Graphics from CPAN?

Sheldon

On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:

> Sheldon McKay wrote:
>>
>> Hi Wes,
>>
>> It looks like it might have something to to with the configuration
>> file.  Could you update your bioperl to a new svn checkout of bioperl-live
>> and also have you changed the configuration files at all?
>
> Hi Sheldon,
>
> I updated bioperl using the latest svn checkout.  This required me
> to update several perl modules as well.  Now I'm completely
> up-to-date.
>
> I'm not seeing any difference in gbrowse_syn.  I'm getting these
> errors in my apache error log file:
>
> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
> Bio::Graphics::Browser::Synteny::shellwords redefined at
> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
> line 11
> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
> <DATA> line 192.
> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
> /htdocs/gbrowse/gbrowse_syn.cgi line 27
> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
> Bio::Graphics::Browser::Synteny::shellwords redefined at
> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
> line 11
> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
> <DATA> line 192.
> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
> /htdocs/gbrowse/gbrowse_syn.cgi line 27
> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
> at
> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
> line 806.
>
> The only change that I have made to the three .conf files is to
> change the -dsn args from "localhost" to the name of our database
> server which runs mysql.
>
>> Sheldon
>>
>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...> wrote:
>>>
>>> Hi,
>>>
>>> I have followed the excellent Gbrowse_syn tutorial
>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>> a working local copy of the sample rice/wild_rice synteny browser
>>> working.  I have successfully completed all steps.  However, the
>>> final gbrowse_syn/oryza display does not display the overview
>>> or synteny display.  The following errors are displayed in the
>>> apache error log:
>>>
>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>> line 11
>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>> <DATA> line 192.
>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27
>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
>>> at
>>>
>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>> line 806.
>>>
>>> Do the above errors mean anything to anywone?
>>>
>>> I have upgraded Exporter to the latest version (5.63).
>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>> I am running bioperl 1.6.
>>>
>>> --
>>> Wes Barris <wes.barris@...>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
>>> focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse@...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>
>
> --
> Wes Barris <wes.barris@...>
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Sheldon McKay wrote:
> Hi Wes,
>
> The shellwords error messages are not related, I think.  One more
> question I forgot to ask: did you update Bio::Graphics from CPAN?

No, I didn't.  Should I?

> Sheldon
>
> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:
>> Sheldon McKay wrote:
>>> Hi Wes,
>>>
>>> It looks like it might have something to to with the configuration
>>> file.  Could you update your bioperl to a new svn checkout of bioperl-live
>>> and also have you changed the configuration files at all?
>> Hi Sheldon,
>>
>> I updated bioperl using the latest svn checkout.  This required me
>> to update several perl modules as well.  Now I'm completely
>> up-to-date.
>>
>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>> errors in my apache error log file:
>>
>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>> line 11
>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>> <DATA> line 192.
>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>> line 11
>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>> <DATA> line 192.
>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
>> at
>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>> line 806.
>>
>> The only change that I have made to the three .conf files is to
>> change the -dsn args from "localhost" to the name of our database
>> server which runs mysql.
>>
>>> Sheldon
>>>
>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...> wrote:
>>>> Hi,
>>>>
>>>> I have followed the excellent Gbrowse_syn tutorial
>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>> working.  I have successfully completed all steps.  However, the
>>>> final gbrowse_syn/oryza display does not display the overview
>>>> or synteny display.  The following errors are displayed in the
>>>> apache error log:
>>>>
>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>> line 11
>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>> <DATA> line 192.
>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27
>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
>>>> at
>>>>
>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>> line 806.
>>>>
>>>> Do the above errors mean anything to anywone?
>>>>
>>>> I have upgraded Exporter to the latest version (5.63).
>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>> I am running bioperl 1.6.
>>>>
>>>> --
>>>> Wes Barris <wes.barris@...>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>> 30-Day
>>>> trial. Simplify your report design, integration and deployment - and
>>>> focus on
>>>> what you do best, core application coding. Discover what's new with
>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> Gmod-gbrowse@...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>
>
>

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Can't hurt!

On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:

> Sheldon McKay wrote:
>>
>> Hi Wes,
>>
>> The shellwords error messages are not related, I think.  One more
>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>
> No, I didn't.  Should I?
>
>> Sheldon
>>
>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:
>>>
>>> Sheldon McKay wrote:
>>>>
>>>> Hi Wes,
>>>>
>>>> It looks like it might have something to to with the configuration
>>>> file.  Could you update your bioperl to a new svn checkout of
>>>> bioperl-live
>>>> and also have you changed the configuration files at all?
>>>
>>> Hi Sheldon,
>>>
>>> I updated bioperl using the latest svn checkout.  This required me
>>> to update several perl modules as well.  Now I'm completely
>>> up-to-date.
>>>
>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>> errors in my apache error log file:
>>>
>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>
>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>> line 11
>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>> <DATA> line 192.
>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>
>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>> line 11
>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>> <DATA> line 192.
>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>> element
>>> at
>>>
>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>> line 806.
>>>
>>> The only change that I have made to the three .conf files is to
>>> change the -dsn args from "localhost" to the name of our database
>>> server which runs mysql.
>>>
>>>> Sheldon
>>>>
>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>> working.  I have successfully completed all steps.  However, the
>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>> or synteny display.  The following errors are displayed in the
>>>>> apache error log:
>>>>>
>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>
>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>> line 11
>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>> <DATA> line 192.
>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27
>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>> element
>>>>> at
>>>>>
>>>>>
>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>> line 806.
>>>>>
>>>>> Do the above errors mean anything to anywone?
>>>>>
>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>> I am running bioperl 1.6.
>>>>>
>>>>> --
>>>>> Wes Barris <wes.barris@...>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>>> 30-Day
>>>>> trial. Simplify your report design, integration and deployment - and
>>>>> focus on
>>>>> what you do best, core application coding. Discover what's new with
>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> Gmod-gbrowse@...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>
>>>>
>>>
>>> --
>>> Wes Barris <wes.barris@...>
>>>
>>
>>
>>
>
>
> --
> Wes Barris <wes.barris@...>
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Sheldon McKay wrote:
> Can't hurt!

I just installed Bio-Graphics-1.982 from CPAN and now everything
is broke.  I can no longer even view a regular gbrowse database.
I'll try some older versions of Bio-Graphics and see if I can
get our site up and running again.

> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:
>> Sheldon McKay wrote:
>>> Hi Wes,
>>>
>>> The shellwords error messages are not related, I think.  One more
>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>> No, I didn't.  Should I?
>>
>>> Sheldon
>>>
>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:
>>>> Sheldon McKay wrote:
>>>>> Hi Wes,
>>>>>
>>>>> It looks like it might have something to to with the configuration
>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>> bioperl-live
>>>>> and also have you changed the configuration files at all?
>>>> Hi Sheldon,
>>>>
>>>> I updated bioperl using the latest svn checkout.  This required me
>>>> to update several perl modules as well.  Now I'm completely
>>>> up-to-date.
>>>>
>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>> errors in my apache error log file:
>>>>
>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>
>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>> line 11
>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>> <DATA> line 192.
>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>
>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>> line 11
>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>> <DATA> line 192.
>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>> element
>>>> at
>>>>
>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>> line 806.
>>>>
>>>> The only change that I have made to the three .conf files is to
>>>> change the -dsn args from "localhost" to the name of our database
>>>> server which runs mysql.
>>>>
>>>>> Sheldon
>>>>>
>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>>> working.  I have successfully completed all steps.  However, the
>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>> or synteny display.  The following errors are displayed in the
>>>>>> apache error log:
>>>>>>
>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>> line 11
>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>>> <DATA> line 192.
>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug 27
>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>> element
>>>>>> at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>> line 806.
>>>>>>
>>>>>> Do the above errors mean anything to anywone?
>>>>>>
>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>>> I am running bioperl 1.6.
>>>>>>
>>>>>> --
>>>>>> Wes Barris <wes.barris@...>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>>>> 30-Day
>>>>>> trial. Simplify your report design, integration and deployment - and
>>>>>> focus on
>>>>>> what you do best, core application coding. Discover what's new with
>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> Gmod-gbrowse@...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>
>>>> --
>>>> Wes Barris <wes.barris@...>
>>>>
>>>
>>>
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>
>
>

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Just to confirm, you are running Gbrowse 1.7?

Sheldon

On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:

> Sheldon McKay wrote:
>>
>> Can't hurt!
>
> I just installed Bio-Graphics-1.982 from CPAN and now everything
> is broke.  I can no longer even view a regular gbrowse database.
> I'll try some older versions of Bio-Graphics and see if I can
> get our site up and running again.
>
>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:
>>>
>>> Sheldon McKay wrote:
>>>>
>>>> Hi Wes,
>>>>
>>>> The shellwords error messages are not related, I think.  One more
>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>
>>> No, I didn't.  Should I?
>>>
>>>> Sheldon
>>>>
>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:
>>>>>
>>>>> Sheldon McKay wrote:
>>>>>>
>>>>>> Hi Wes,
>>>>>>
>>>>>> It looks like it might have something to to with the configuration
>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>> bioperl-live
>>>>>> and also have you changed the configuration files at all?
>>>>>
>>>>> Hi Sheldon,
>>>>>
>>>>> I updated bioperl using the latest svn checkout.  This required me
>>>>> to update several perl modules as well.  Now I'm completely
>>>>> up-to-date.
>>>>>
>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>> errors in my apache error log file:
>>>>>
>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>
>>>>>
>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>> line 11
>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>> <DATA> line 192.
>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>
>>>>>
>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>> line 11
>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>> <DATA> line 192.
>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>> element
>>>>> at
>>>>>
>>>>>
>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>> line 806.
>>>>>
>>>>> The only change that I have made to the three .conf files is to
>>>>> change the -dsn args from "localhost" to the name of our database
>>>>> server which runs mysql.
>>>>>
>>>>>> Sheldon
>>>>>>
>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>>>> working.  I have successfully completed all steps.  However, the
>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>> apache error log:
>>>>>>>
>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>> Subroutine
>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>> line 11
>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>> Subroutine
>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>> 67,
>>>>>>> <DATA> line 192.
>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug
>>>>>>> 27
>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>> element
>>>>>>> at
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>> line 806.
>>>>>>>
>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>
>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>>>> I am running bioperl 1.6.
>>>>>>>
>>>>>>> --
>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>>>>> 30-Day
>>>>>>> trial. Simplify your report design, integration and deployment - and
>>>>>>> focus on
>>>>>>> what you do best, core application coding. Discover what's new with
>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>> _______________________________________________
>>>>>>> Gmod-gbrowse mailing list
>>>>>>> Gmod-gbrowse@...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>
>>>>>>
>>>>> --
>>>>> Wes Barris <wes.barris@...>
>>>>>
>>>>
>>>>
>>>
>>> --
>>> Wes Barris <wes.barris@...>
>>>
>>
>>
>>
>
>
> --
> Wes Barris <wes.barris@...>
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Sheldon McKay wrote:
> Just to confirm, you are running Gbrowse 1.7?

Yes.  I found why all of our 50+ databases broke.  The upgrade of
Bio::Graphics is incompatible with '#' characters in code like
this:

                elsif ($notes =~ /($chr)38/) { return '#ffff00'; }
                elsif ($notes =~ /($chr)37/) { return '#eeff22'; }

I'm looking for an alternative now.  Unfortunately, we use this
notation in many of our databases.

> Sheldon
>
> On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:
>> Sheldon McKay wrote:
>>> Can't hurt!
>> I just installed Bio-Graphics-1.982 from CPAN and now everything
>> is broke.  I can no longer even view a regular gbrowse database.
>> I'll try some older versions of Bio-Graphics and see if I can
>> get our site up and running again.
>>
>>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:
>>>> Sheldon McKay wrote:
>>>>> Hi Wes,
>>>>>
>>>>> The shellwords error messages are not related, I think.  One more
>>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>> No, I didn't.  Should I?
>>>>
>>>>> Sheldon
>>>>>
>>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:
>>>>>> Sheldon McKay wrote:
>>>>>>> Hi Wes,
>>>>>>>
>>>>>>> It looks like it might have something to to with the configuration
>>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>>> bioperl-live
>>>>>>> and also have you changed the configuration files at all?
>>>>>> Hi Sheldon,
>>>>>>
>>>>>> I updated bioperl using the latest svn checkout.  This required me
>>>>>> to update several perl modules as well.  Now I'm completely
>>>>>> up-to-date.
>>>>>>
>>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>>> errors in my apache error log file:
>>>>>>
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>> line 11
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>>> <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>> line 11
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>>> <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
>>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>> element
>>>>>> at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>> line 806.
>>>>>>
>>>>>> The only change that I have made to the three .conf files is to
>>>>>> change the -dsn args from "localhost" to the name of our database
>>>>>> server which runs mysql.
>>>>>>
>>>>>>> Sheldon
>>>>>>>
>>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
>>>>>>> wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>>>>> working.  I have successfully completed all steps.  However, the
>>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>>> apache error log:
>>>>>>>>
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>>> line 11
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>>> 67,
>>>>>>>> <DATA> line 192.
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug
>>>>>>>> 27
>>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>>> element
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>>> line 806.
>>>>>>>>
>>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>>
>>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>>>>> I am running bioperl 1.6.
>>>>>>>>
>>>>>>>> --
>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>>>>>> 30-Day
>>>>>>>> trial. Simplify your report design, integration and deployment - and
>>>>>>>> focus on
>>>>>>>> what you do best, core application coding. Discover what's new with
>>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> Gmod-gbrowse@...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>
>>>>>> --
>>>>>> Wes Barris <wes.barris@...>
>>>>>>
>>>>>
>>>> --
>>>> Wes Barris <wes.barris@...>
>>>>
>>>
>>>
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>
>
>

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Scott Cain-4]

Hi Wes,

A work around for the # thing is to express it as an chr, like so:

    ... return chr(35).'ffff00';

Ugly, but it works.

Scott

On Aug 27, 2009, at 10:09 PM, Wes Barris wrote:

> Sheldon McKay wrote:
>> Just to confirm, you are running Gbrowse 1.7?
>
> Yes.  I found why all of our 50+ databases broke.  The upgrade of
> Bio::Graphics is incompatible with '#' characters in code like
> this:
>
>                elsif ($notes =~ /($chr)38/) { return '#ffff00'; }
>                elsif ($notes =~ /($chr)37/) { return '#eeff22'; }
>
> I'm looking for an alternative now.  Unfortunately, we use this
> notation in many of our databases.
>
>> Sheldon
>>
>> On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...>  
>> wrote:
>>> Sheldon McKay wrote:
>>>> Can't hurt!
>>> I just installed Bio-Graphics-1.982 from CPAN and now everything
>>> is broke.  I can no longer even view a regular gbrowse database.
>>> I'll try some older versions of Bio-Graphics and see if I can
>>> get our site up and running again.
>>>
>>>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...>  
>>>> wrote:
>>>>> Sheldon McKay wrote:
>>>>>> Hi Wes,
>>>>>>
>>>>>> The shellwords error messages are not related, I think.  One more
>>>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>>> No, I didn't.  Should I?
>>>>>
>>>>>> Sheldon
>>>>>>
>>>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes  
>>>>>> Barris<wes.barris@...> wrote:
>>>>>>> Sheldon McKay wrote:
>>>>>>>> Hi Wes,
>>>>>>>>
>>>>>>>> It looks like it might have something to to with the  
>>>>>>>> configuration
>>>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>>>> bioperl-live
>>>>>>>> and also have you changed the configuration files at all?
>>>>>>> Hi Sheldon,
>>>>>>>
>>>>>>> I updated bioperl using the latest svn checkout.  This  
>>>>>>> required me
>>>>>>> to update several perl modules as well.  Now I'm completely
>>>>>>> up-to-date.
>>>>>>>
>>>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>>>> errors in my apache error log file:
>>>>>>>
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  
>>>>>>> Subroutine
>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>> Graphics/Browser/Synteny.pm
>>>>>>> line 11
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  
>>>>>>> Subroutine
>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm  
>>>>>>> line 67,
>>>>>>> <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  
>>>>>>> Subroutine
>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>> Graphics/Browser/Synteny.pm
>>>>>>> line 11
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  
>>>>>>> Subroutine
>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm  
>>>>>>> line 67,
>>>>>>> <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217]  
>>>>>>> [Fri Aug 28
>>>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in  
>>>>>>> hash
>>>>>>> element
>>>>>>> at
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>> Graphics/FeatureFile.pm
>>>>>>> line 806.
>>>>>>>
>>>>>>> The only change that I have made to the three .conf files is to
>>>>>>> change the -dsn args from "localhost" to the name of our  
>>>>>>> database
>>>>>>> server which runs mysql.
>>>>>>>
>>>>>>>> Sheldon
>>>>>>>>
>>>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes  
>>>>>>>> Barris<wes.barris@...>
>>>>>>>> wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>>>> a working local copy of the sample rice/wild_rice synteny  
>>>>>>>>> browser
>>>>>>>>> working.  I have successfully completed all steps.  However,  
>>>>>>>>> the
>>>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>>>> apache error log:
>>>>>>>>>
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>> Subroutine
>>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  
>>>>>>>>> at
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>>> Graphics/Browser/Synteny.pm
>>>>>>>>> line 11
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>> Subroutine
>>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/
>>>>>>>>> Exporter.pm line
>>>>>>>>> 67,
>>>>>>>>> <DATA> line 192.
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  
>>>>>>>>> at
>>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217]  
>>>>>>>>> [Thu Aug
>>>>>>>>> 27
>>>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value  
>>>>>>>>> in hash
>>>>>>>>> element
>>>>>>>>> at
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>>> Graphics/FeatureFile.pm
>>>>>>>>> line 806.
>>>>>>>>>
>>>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>>>
>>>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>>>> I am running the latest gbrowse from CVS (downloaded  
>>>>>>>>> yesterday).
>>>>>>>>> I am running bioperl 1.6.
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Let Crystal Reports handle the reporting - Free Crystal  
>>>>>>>>> Reports 2008
>>>>>>>>> 30-Day
>>>>>>>>> trial. Simplify your report design, integration and  
>>>>>>>>> deployment - and
>>>>>>>>> focus on
>>>>>>>>> what you do best, core application coding. Discover what's  
>>>>>>>>> new with
>>>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>>> Gmod-gbrowse@...
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>>
>>>>>>> --
>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>
>>>>>>
>>>>> --
>>>>> Wes Barris <wes.barris@...>
>>>>>
>>>>
>>>>
>>>
>>> --
>>> Wes Barris <wes.barris@...>
>>>
>>
>>
>>
>
>
> --
> Wes Barris <wes.barris@...>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> 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





------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Scott Cain wrote:
> Hi Wes,
>
> A work around for the # thing is to express it as an chr, like so:
>
>     ... return chr(35).'ffff00';
>
> Ugly, but it works.

Thanks Scott.  Yes, I'm going through all of my files and modifying
them like this.

> Scott
>
> On Aug 27, 2009, at 10:09 PM, Wes Barris wrote:
>
>> Sheldon McKay wrote:
>>> Just to confirm, you are running Gbrowse 1.7?
>> Yes.  I found why all of our 50+ databases broke.  The upgrade of
>> Bio::Graphics is incompatible with '#' characters in code like
>> this:
>>
>>                elsif ($notes =~ /($chr)38/) { return '#ffff00'; }
>>                elsif ($notes =~ /($chr)37/) { return '#eeff22'; }
>>
>> I'm looking for an alternative now.  Unfortunately, we use this
>> notation in many of our databases.
>>
>>> Sheldon
>>>
>>> On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...>  
>>> wrote:
>>>> Sheldon McKay wrote:
>>>>> Can't hurt!
>>>> I just installed Bio-Graphics-1.982 from CPAN and now everything
>>>> is broke.  I can no longer even view a regular gbrowse database.
>>>> I'll try some older versions of Bio-Graphics and see if I can
>>>> get our site up and running again.
>>>>
>>>>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...>  
>>>>> wrote:
>>>>>> Sheldon McKay wrote:
>>>>>>> Hi Wes,
>>>>>>>
>>>>>>> The shellwords error messages are not related, I think.  One more
>>>>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>>>> No, I didn't.  Should I?
>>>>>>
>>>>>>> Sheldon
>>>>>>>
>>>>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes  
>>>>>>> Barris<wes.barris@...> wrote:
>>>>>>>> Sheldon McKay wrote:
>>>>>>>>> Hi Wes,
>>>>>>>>>
>>>>>>>>> It looks like it might have something to to with the  
>>>>>>>>> configuration
>>>>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>>>>> bioperl-live
>>>>>>>>> and also have you changed the configuration files at all?
>>>>>>>> Hi Sheldon,
>>>>>>>>
>>>>>>>> I updated bioperl using the latest svn checkout.  This  
>>>>>>>> required me
>>>>>>>> to update several perl modules as well.  Now I'm completely
>>>>>>>> up-to-date.
>>>>>>>>
>>>>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>>>>> errors in my apache error log file:
>>>>>>>>
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  
>>>>>>>> Subroutine
>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>> Graphics/Browser/Synteny.pm
>>>>>>>> line 11
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  
>>>>>>>> Subroutine
>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm  
>>>>>>>> line 67,
>>>>>>>> <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  
>>>>>>>> Subroutine
>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>> Graphics/Browser/Synteny.pm
>>>>>>>> line 11
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  
>>>>>>>> Subroutine
>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm  
>>>>>>>> line 67,
>>>>>>>> <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217]  
>>>>>>>> [Fri Aug 28
>>>>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in  
>>>>>>>> hash
>>>>>>>> element
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>> Graphics/FeatureFile.pm
>>>>>>>> line 806.
>>>>>>>>
>>>>>>>> The only change that I have made to the three .conf files is to
>>>>>>>> change the -dsn args from "localhost" to the name of our  
>>>>>>>> database
>>>>>>>> server which runs mysql.
>>>>>>>>
>>>>>>>>> Sheldon
>>>>>>>>>
>>>>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes  
>>>>>>>>> Barris<wes.barris@...>
>>>>>>>>> wrote:
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>>>>> a working local copy of the sample rice/wild_rice synteny  
>>>>>>>>>> browser
>>>>>>>>>> working.  I have successfully completed all steps.  However,  
>>>>>>>>>> the
>>>>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>>>>> apache error log:
>>>>>>>>>>
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>>> Subroutine
>>>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>>>> Graphics/Browser/Synteny.pm
>>>>>>>>>> line 11
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>>> Subroutine
>>>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/
>>>>>>>>>> Exporter.pm line
>>>>>>>>>> 67,
>>>>>>>>>> <DATA> line 192.
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  
>>>>>>>>>> at
>>>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217]  
>>>>>>>>>> [Thu Aug
>>>>>>>>>> 27
>>>>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value  
>>>>>>>>>> in hash
>>>>>>>>>> element
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/
>>>>>>>>>> Graphics/FeatureFile.pm
>>>>>>>>>> line 806.
>>>>>>>>>>
>>>>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>>>>
>>>>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>>>>> I am running the latest gbrowse from CVS (downloaded  
>>>>>>>>>> yesterday).
>>>>>>>>>> I am running bioperl 1.6.
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> Let Crystal Reports handle the reporting - Free Crystal  
>>>>>>>>>> Reports 2008
>>>>>>>>>> 30-Day
>>>>>>>>>> trial. Simplify your report design, integration and  
>>>>>>>>>> deployment - and
>>>>>>>>>> focus on
>>>>>>>>>> what you do best, core application coding. Discover what's  
>>>>>>>>>> new with
>>>>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>>>> Gmod-gbrowse@...
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>>>
>>>>>>>> --
>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>
>>>>>> --
>>>>>> Wes Barris <wes.barris@...>
>>>>>>
>>>>>
>>>> --
>>>> Wes Barris <wes.barris@...>
>>>>
>>>
>>>
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and  
>> focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> 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
>
>
>
>

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Sheldon McKay wrote:
> Just to confirm, you are running Gbrowse 1.7?

Ok.  I have recovered from the Bio-Graphics-1.982 install.  I have
edited all of my other .conf files so that there are no errors reported
in the apache log file when viewing normal gbrowse databases.

Now, back to gbrowse_syn.  When gbrowse_syn is used to view the
oryza database, these errors are logged by apache:

[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine Bio::Graphics::Browser::Synteny::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm line 11
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at /htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 14:17:31 2009] [error] [client 140.253.153.217] [Fri Aug 28 14:17:31 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element at
/usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006.

I don't receive the "shellwords" errors with viewing gbrowse
databases.

The URL that can be used to see the results is:

http://www.livestockgenomics.csiro.au/perl/gbrowse_syn.cgi/oryza/

I have the absolute latest versions of bioperl, gbrowse, biographics
and any dependencies required by bioperl.

The only differences between the provided .conf files and what I am
running has to do with the location of the database server:

wes@bioactive> diff /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/oryza.synconf oryza.synconf
5c5
< join        = dbi:mysql:database=rice_synteny;host=localhost;user=nobody
---
 > join        = dbi:mysql:database=rice_synteny;host=biodata.sl.csiro.au;user=nobody
wes@bioactive> diff /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/rice.conf rice.conf
5c5
<                      -dsn     dbi:mysql:rice;host=localhost
---
 >                      -dsn     dbi:mysql:rice;host=biodata.sl.csiro.au
wes@bioactive> diff /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/wild_rice.conf wild_rice.conf
5c5
<                      -dsn     dbi:mysql:wild_rice;host=localhost
---
 >                      -dsn     dbi:mysql:wild_rice;host=biodata.sl.csiro.au

> Sheldon
>
> On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:
>> Sheldon McKay wrote:
>>> Can't hurt!
>> I just installed Bio-Graphics-1.982 from CPAN and now everything
>> is broke.  I can no longer even view a regular gbrowse database.
>> I'll try some older versions of Bio-Graphics and see if I can
>> get our site up and running again.
>>
>>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:
>>>> Sheldon McKay wrote:
>>>>> Hi Wes,
>>>>>
>>>>> The shellwords error messages are not related, I think.  One more
>>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>> No, I didn't.  Should I?
>>>>
>>>>> Sheldon
>>>>>
>>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...> wrote:
>>>>>> Sheldon McKay wrote:
>>>>>>> Hi Wes,
>>>>>>>
>>>>>>> It looks like it might have something to to with the configuration
>>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>>> bioperl-live
>>>>>>> and also have you changed the configuration files at all?
>>>>>> Hi Sheldon,
>>>>>>
>>>>>> I updated bioperl using the latest svn checkout.  This required me
>>>>>> to update several perl modules as well.  Now I'm completely
>>>>>> up-to-date.
>>>>>>
>>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>>> errors in my apache error log file:
>>>>>>
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>> line 11
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>>> <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>> line 11
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217] Subroutine
>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>>>>>> <DATA> line 192.
>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug 28
>>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>> element
>>>>>> at
>>>>>>
>>>>>>
>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>> line 806.
>>>>>>
>>>>>> The only change that I have made to the three .conf files is to
>>>>>> change the -dsn args from "localhost" to the name of our database
>>>>>> server which runs mysql.
>>>>>>
>>>>>>> Sheldon
>>>>>>>
>>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
>>>>>>> wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>>>>> working.  I have successfully completed all steps.  However, the
>>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>>> apache error log:
>>>>>>>>
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>>> line 11
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>>> 67,
>>>>>>>> <DATA> line 192.
>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu Aug
>>>>>>>> 27
>>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>>> element
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>>> line 806.
>>>>>>>>
>>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>>
>>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>>>>> I am running bioperl 1.6.
>>>>>>>>
>>>>>>>> --
>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>>>>>> 30-Day
>>>>>>>> trial. Simplify your report design, integration and deployment - and
>>>>>>>> focus on
>>>>>>>> what you do best, core application coding. Discover what's new with
>>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> Gmod-gbrowse@...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>
>>>>>> --
>>>>>> Wes Barris <wes.barris@...>
>>>>>>
>>>>>
>>>> --
>>>> Wes Barris <wes.barris@...>
>>>>
>>>
>>>
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>
>
>

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Hi Wes,

The URL you provided was working when I checked it.  A CVS update
should silence the annoying but harmless 'shellwords' squawks.  The
'Use of uninitialized value in hash element at
/usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006'
error is a symptom of specifying a search source (species) that does
not exist in the configuration file.  I added a sanity check here so
that a warning will be thrown when a specified data source is not
known or configured.

Sheldon


On Fri, Aug 28, 2009 at 12:23 AM, Wes Barris<wes.barris@...> wrote:

> Sheldon McKay wrote:
>>
>> Just to confirm, you are running Gbrowse 1.7?
>
> Ok.  I have recovered from the Bio-Graphics-1.982 install.  I have
> edited all of my other .conf files so that there are no errors reported
> in the apache log file when viewing normal gbrowse databases.
>
> Now, back to gbrowse_syn.  When gbrowse_syn is used to view the
> oryza database, these errors are logged by apache:
>
> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
> Bio::Graphics::Browser::Synteny::shellwords redefined at
> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
> line 11
> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
> <DATA> line 192.
> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
> /htdocs/gbrowse/gbrowse_syn.cgi line 27
> [Fri Aug 28 14:17:31 2009] [error] [client 140.253.153.217] [Fri Aug 28
> 14:17:31 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
> at /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006.
>
> I don't receive the "shellwords" errors with viewing gbrowse
> databases.
>
> The URL that can be used to see the results is:
>
> http://www.livestockgenomics.csiro.au/perl/gbrowse_syn.cgi/oryza/
>
> I have the absolute latest versions of bioperl, gbrowse, biographics
> and any dependencies required by bioperl.
>
> The only differences between the provided .conf files and what I am
> running has to do with the location of the database server:
>
> wes@bioactive> diff
> /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/oryza.synconf
> oryza.synconf
> 5c5
> < join        = dbi:mysql:database=rice_synteny;host=localhost;user=nobody
> ---
>> join        =
>> dbi:mysql:database=rice_synteny;host=biodata.sl.csiro.au;user=nobody
> wes@bioactive> diff
> /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/rice.conf
> rice.conf
> 5c5
> <                      -dsn     dbi:mysql:rice;host=localhost
> ---
>>                      -dsn     dbi:mysql:rice;host=biodata.sl.csiro.au
> wes@bioactive> diff
> /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/wild_rice.conf
> wild_rice.conf
> 5c5
> <                      -dsn     dbi:mysql:wild_rice;host=localhost
> ---
>>                      -dsn     dbi:mysql:wild_rice;host=biodata.sl.csiro.au
>
>
>> Sheldon
>>
>> On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:
>>>
>>> Sheldon McKay wrote:
>>>>
>>>> Can't hurt!
>>>
>>> I just installed Bio-Graphics-1.982 from CPAN and now everything
>>> is broke.  I can no longer even view a regular gbrowse database.
>>> I'll try some older versions of Bio-Graphics and see if I can
>>> get our site up and running again.
>>>
>>>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:
>>>>>
>>>>> Sheldon McKay wrote:
>>>>>>
>>>>>> Hi Wes,
>>>>>>
>>>>>> The shellwords error messages are not related, I think.  One more
>>>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>>>
>>>>> No, I didn't.  Should I?
>>>>>
>>>>>> Sheldon
>>>>>>
>>>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...>
>>>>>> wrote:
>>>>>>>
>>>>>>> Sheldon McKay wrote:
>>>>>>>>
>>>>>>>> Hi Wes,
>>>>>>>>
>>>>>>>> It looks like it might have something to to with the configuration
>>>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>>>> bioperl-live
>>>>>>>> and also have you changed the configuration files at all?
>>>>>>>
>>>>>>> Hi Sheldon,
>>>>>>>
>>>>>>> I updated bioperl using the latest svn checkout.  This required me
>>>>>>> to update several perl modules as well.  Now I'm completely
>>>>>>> up-to-date.
>>>>>>>
>>>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>>>> errors in my apache error log file:
>>>>>>>
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
>>>>>>> Subroutine
>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>> line 11
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
>>>>>>> Subroutine
>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>> 67,
>>>>>>> <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
>>>>>>> Subroutine
>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>> line 11
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
>>>>>>> Subroutine
>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>> 67,
>>>>>>> <DATA> line 192.
>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug
>>>>>>> 28
>>>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>> element
>>>>>>> at
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>> line 806.
>>>>>>>
>>>>>>> The only change that I have made to the three .conf files is to
>>>>>>> change the -dsn args from "localhost" to the name of our database
>>>>>>> server which runs mysql.
>>>>>>>
>>>>>>>> Sheldon
>>>>>>>>
>>>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>>>>>> working.  I have successfully completed all steps.  However, the
>>>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>>>> apache error log:
>>>>>>>>>
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>> Subroutine
>>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>>>> line 11
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>> Subroutine
>>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>>>> 67,
>>>>>>>>> <DATA> line 192.
>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu
>>>>>>>>> Aug
>>>>>>>>> 27
>>>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>>>> element
>>>>>>>>> at
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>>>> line 806.
>>>>>>>>>
>>>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>>>
>>>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>>>>>> I am running bioperl 1.6.
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports
>>>>>>>>> 2008
>>>>>>>>> 30-Day
>>>>>>>>> trial. Simplify your report design, integration and deployment -
>>>>>>>>> and
>>>>>>>>> focus on
>>>>>>>>> what you do best, core application coding. Discover what's new with
>>>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>>> Gmod-gbrowse@...
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>>
>>>>>>> --
>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>
>>>>>>
>>>>> --
>>>>> Wes Barris <wes.barris@...>
>>>>>
>>>>
>>>>
>>>
>>> --
>>> Wes Barris <wes.barris@...>
>>>
>>
>>
>>
>
>
> --
> Wes Barris <wes.barris@...>
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Wes Barris]

Sheldon McKay wrote:

> Hi Wes,
>
> The URL you provided was working when I checked it.  A CVS update
> should silence the annoying but harmless 'shellwords' squawks.  The
> 'Use of uninitialized value in hash element at
> /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006'
> error is a symptom of specifying a search source (species) that does
> not exist in the configuration file.  I added a sanity check here so
> that a warning will be thrown when a specified data source is not
> known or configured.

Thanks Sheldon.  A CVS update has stopped the apache error messages from
occurring.  Also, as you state, gbrowse_syn is working.

The initial display of gbrowse_syn contains an error "Species 'nosrc'
is not configured for this database" and doesn't show a synteny
alignment until one selects an example region.  This led me to believe
that it wasn't working.

I had just finished trying to get both synbrowse and synview working.
When both of those failed I guess that I was just expecting gbrowse_syn
to fail too.

> Sheldon
>
>
> On Fri, Aug 28, 2009 at 12:23 AM, Wes Barris<wes.barris@...> wrote:
>> Sheldon McKay wrote:
>>> Just to confirm, you are running Gbrowse 1.7?
>> Ok.  I have recovered from the Bio-Graphics-1.982 install.  I have
>> edited all of my other .conf files so that there are no errors reported
>> in the apache log file when viewing normal gbrowse databases.
>>
>> Now, back to gbrowse_syn.  When gbrowse_syn is used to view the
>> oryza database, these errors are logged by apache:
>>
>> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>> line 11
>> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
>> <DATA> line 192.
>> [Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>> [Fri Aug 28 14:17:31 2009] [error] [client 140.253.153.217] [Fri Aug 28
>> 14:17:31 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
>> at /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006.
>>
>> I don't receive the "shellwords" errors with viewing gbrowse
>> databases.
>>
>> The URL that can be used to see the results is:
>>
>> http://www.livestockgenomics.csiro.au/perl/gbrowse_syn.cgi/oryza/
>>
>> I have the absolute latest versions of bioperl, gbrowse, biographics
>> and any dependencies required by bioperl.
>>
>> The only differences between the provided .conf files and what I am
>> running has to do with the location of the database server:
>>
>> wes@bioactive> diff
>> /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/oryza.synconf
>> oryza.synconf
>> 5c5
>> < join        = dbi:mysql:database=rice_synteny;host=localhost;user=nobody
>> ---
>>> join        =
>>> dbi:mysql:database=rice_synteny;host=biodata.sl.csiro.au;user=nobody
>> wes@bioactive> diff
>> /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/rice.conf
>> rice.conf
>> 5c5
>> <                      -dsn     dbi:mysql:rice;host=localhost
>> ---
>>>                      -dsn     dbi:mysql:rice;host=biodata.sl.csiro.au
>> wes@bioactive> diff
>> /usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/wild_rice.conf
>> wild_rice.conf
>> 5c5
>> <                      -dsn     dbi:mysql:wild_rice;host=localhost
>> ---
>>>                      -dsn     dbi:mysql:wild_rice;host=biodata.sl.csiro.au
>>
>>> Sheldon
>>>
>>> On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:
>>>> Sheldon McKay wrote:
>>>>> Can't hurt!
>>>> I just installed Bio-Graphics-1.982 from CPAN and now everything
>>>> is broke.  I can no longer even view a regular gbrowse database.
>>>> I'll try some older versions of Bio-Graphics and see if I can
>>>> get our site up and running again.
>>>>
>>>>> On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:
>>>>>> Sheldon McKay wrote:
>>>>>>> Hi Wes,
>>>>>>>
>>>>>>> The shellwords error messages are not related, I think.  One more
>>>>>>> question I forgot to ask: did you update Bio::Graphics from CPAN?
>>>>>> No, I didn't.  Should I?
>>>>>>
>>>>>>> Sheldon
>>>>>>>
>>>>>>> On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...>
>>>>>>> wrote:
>>>>>>>> Sheldon McKay wrote:
>>>>>>>>> Hi Wes,
>>>>>>>>>
>>>>>>>>> It looks like it might have something to to with the configuration
>>>>>>>>> file.  Could you update your bioperl to a new svn checkout of
>>>>>>>>> bioperl-live
>>>>>>>>> and also have you changed the configuration files at all?
>>>>>>>> Hi Sheldon,
>>>>>>>>
>>>>>>>> I updated bioperl using the latest svn checkout.  This required me
>>>>>>>> to update several perl modules as well.  Now I'm completely
>>>>>>>> up-to-date.
>>>>>>>>
>>>>>>>> I'm not seeing any difference in gbrowse_syn.  I'm getting these
>>>>>>>> errors in my apache error log file:
>>>>>>>>
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>>> line 11
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>>> 67,
>>>>>>>> <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>>> line 11
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
>>>>>>>> Subroutine
>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>>> 67,
>>>>>>>> <DATA> line 192.
>>>>>>>> [Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>> [Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug
>>>>>>>> 28
>>>>>>>> 10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>>> element
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>>> line 806.
>>>>>>>>
>>>>>>>> The only change that I have made to the three .conf files is to
>>>>>>>> change the -dsn args from "localhost" to the name of our database
>>>>>>>> server which runs mysql.
>>>>>>>>
>>>>>>>>> Sheldon
>>>>>>>>>
>>>>>>>>> On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
>>>>>>>>> wrote:
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I have followed the excellent Gbrowse_syn tutorial
>>>>>>>>>> http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
>>>>>>>>>> a working local copy of the sample rice/wild_rice synteny browser
>>>>>>>>>> working.  I have successfully completed all steps.  However, the
>>>>>>>>>> final gbrowse_syn/oryza display does not display the overview
>>>>>>>>>> or synteny display.  The following errors are displayed in the
>>>>>>>>>> apache error log:
>>>>>>>>>>
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>>> Subroutine
>>>>>>>>>> Bio::Graphics::Browser::Synteny::shellwords redefined at
>>>>>>>>>> /usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
>>>>>>>>>> line 11
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
>>>>>>>>>> Subroutine
>>>>>>>>>> main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
>>>>>>>>>> 67,
>>>>>>>>>> <DATA> line 192.
>>>>>>>>>> [Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
>>>>>>>>>> /htdocs/gbrowse/gbrowse_syn.cgi line 27
>>>>>>>>>> [Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu
>>>>>>>>>> Aug
>>>>>>>>>> 27
>>>>>>>>>> 11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
>>>>>>>>>> element
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
>>>>>>>>>> line 806.
>>>>>>>>>>
>>>>>>>>>> Do the above errors mean anything to anywone?
>>>>>>>>>>
>>>>>>>>>> I have upgraded Exporter to the latest version (5.63).
>>>>>>>>>> I am running the latest gbrowse from CVS (downloaded yesterday).
>>>>>>>>>> I am running bioperl 1.6.
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports
>>>>>>>>>> 2008
>>>>>>>>>> 30-Day
>>>>>>>>>> trial. Simplify your report design, integration and deployment -
>>>>>>>>>> and
>>>>>>>>>> focus on
>>>>>>>>>> what you do best, core application coding. Discover what's new with
>>>>>>>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>>>> Gmod-gbrowse@...
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>>>
>>>>>>>> --
>>>>>>>> Wes Barris <wes.barris@...>
>>>>>>>>
>>>>>> --
>>>>>> Wes Barris <wes.barris@...>
>>>>>>
>>>>>
>>>> --
>>>> Wes Barris <wes.barris@...>
>>>>
>>>
>>>
>>
>> --
>> Wes Barris <wes.barris@...>
>>
>
>
>
> --
> Sheldon McKay, PhD
> Cold Spring Harbor Laboratory
> Office/Mobile:  [phone]
>
> Sent from Milford, Connecticut, United States

--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Hi Wes,

Thanks for staying the course.  Like Gbrowse, Gbrowse_syn needs to have the species and region specified before it draws anything.  A default segment to be displayed when none is specified can be added to the GBrowse_syn config file.  This is also available (or soon will be) in GBrowse_syn.  The thing I was a bit confused about was that the URL you pointed us to earlier in this thread was working from the first time I visited it.

The 'norsrc' error will not do.  Thanks for pointing that out. 

As for synbrowse, and synview, you may need to contact the authors directly, as I am not sure they monitor this list.

Sheldon

On Thu, Sep 3, 2009 at 12:10 AM, Wes Barris <wes.barris@...> wrote:

Sheldon McKay wrote:

Hi Wes,

The URL you provided was working when I checked it.  A CVS update
should silence the annoying but harmless 'shellwords' squawks.  The
'Use of uninitialized value in hash element at
/usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006'
error is a symptom of specifying a search source (species) that does
not exist in the configuration file.  I added a sanity check here so
that a warning will be thrown when a specified data source is not
known or configured.

Thanks Sheldon.  A CVS update has stopped the apache error messages from
occurring.  Also, as you state, gbrowse_syn is working.

The initial display of gbrowse_syn contains an error "Species 'nosrc'
is not configured for this database" and doesn't show a synteny
alignment until one selects an example region.  This led me to believe
that it wasn't working.

I had just finished trying to get both synbrowse and synview working.
When both of those failed I guess that I was just expecting gbrowse_syn
to fail too.

Sheldon


On Fri, Aug 28, 2009 at 12:23 AM, Wes Barris<wes.barris@...> wrote:

Sheldon McKay wrote:

Just to confirm, you are running Gbrowse 1.7?

Ok.  I have recovered from the Bio-Graphics-1.982 install.  I have
edited all of my other .conf files so that there are no errors reported
in the apache log file when viewing normal gbrowse databases.

Now, back to gbrowse_syn.  When gbrowse_syn is used to view the
oryza database, these errors are logged by apache:

[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
<DATA> line 192.
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 14:17:31 2009] [error] [client 140.253.153.217] [Fri Aug 28
14:17:31 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
at /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006.

I don't receive the "shellwords" errors with viewing gbrowse
databases.

The URL that can be used to see the results is:

http://www.livestockgenomics.csiro.au/perl/gbrowse_syn.cgi/oryza/

I have the absolute latest versions of bioperl, gbrowse, biographics
and any dependencies required by bioperl.

The only differences between the provided .conf files and what I am
running has to do with the location of the database server:

wes@bioactive> diff
/usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/oryza.synconf
oryza.synconf
5c5
< join        = dbi:mysql:database=rice_synteny;host=localhost;user=nobody
---

join        =
dbi:mysql:database=rice_synteny;host=biodata.sl.csiro.au;user=nobody

wes@bioactive> diff
/usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/rice.conf
rice.conf
5c5
<                      -dsn     dbi:mysql:rice;host=localhost
---

                    -dsn     dbi:mysql:rice;host=biodata.sl.csiro.au

wes@bioactive> diff
/usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/wild_rice.conf
wild_rice.conf
5c5
<                      -dsn     dbi:mysql:wild_rice;host=localhost
---

                    -dsn     dbi:mysql:wild_rice;host=biodata.sl.csiro.au

Sheldon

On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:

Sheldon McKay wrote:

Can't hurt!

I just installed Bio-Graphics-1.982 from CPAN and now everything
is broke.  I can no longer even view a regular gbrowse database.
I'll try some older versions of Bio-Graphics and see if I can
get our site up and running again.

On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:

Sheldon McKay wrote:

Hi Wes,

The shellwords error messages are not related, I think.  One more
question I forgot to ask: did you update Bio::Graphics from CPAN?

No, I didn't.  Should I?

Sheldon

On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...>
wrote:

Sheldon McKay wrote:

Hi Wes,

It looks like it might have something to to with the configuration
file.  Could you update your bioperl to a new svn checkout of
bioperl-live
and also have you changed the configuration files at all?

Hi Sheldon,

I updated bioperl using the latest svn checkout.  This required me
to update several perl modules as well.  Now I'm completely
up-to-date.

I'm not seeing any difference in gbrowse_syn.  I'm getting these
errors in my apache error log file:

[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
67,
<DATA> line 192.
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
67,
<DATA> line 192.
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug
28
10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
element
at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
line 806.

The only change that I have made to the three .conf files is to
change the -dsn args from "localhost" to the name of our database
server which runs mysql.

Sheldon

On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
wrote:

Hi,

I have followed the excellent Gbrowse_syn tutorial
http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
a working local copy of the sample rice/wild_rice synteny browser
working.  I have successfully completed all steps.  However, the
final gbrowse_syn/oryza display does not display the overview
or synteny display.  The following errors are displayed in the
apache error log:

[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
67,
<DATA> line 192.
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu
Aug
27
11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
element
at




/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
line 806.

Do the above errors mean anything to anywone?

I have upgraded Exporter to the latest version (5.63).
I am running the latest gbrowse from CVS (downloaded yesterday).
I am running bioperl 1.6.

--
Wes Barris <wes.barris@...>





------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports
2008
30-Day
trial. Simplify your report design, integration and deployment -
and
focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Wes Barris <wes.barris@...>

--
Wes Barris <wes.barris@...>

--
Wes Barris <wes.barris@...>

--
Wes Barris <wes.barris@...>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States

--

Wes Barris <wes.barris@...>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Sheldon McKay-3]

Hi Wes,

I committed a fix to CVS for the 'nosrc' bug.   In the GBrowse2 version of GBrowse_syn, which will come out later this year, there will be a configuration option analogous to the 'initial landmark' option in GBrowse that will load a default data source, species, and segment if none are specified.

Sheldon

On Thu, Sep 3, 2009 at 7:44 AM, Sheldon McKay <sheldon.mckay@...> wrote:

Hi Wes,

Thanks for staying the course.  Like Gbrowse, Gbrowse_syn needs to have the species and region specified before it draws anything.  A default segment to be displayed when none is specified can be added to the GBrowse_syn config file.  This is also available (or soon will be) in GBrowse_syn.  The thing I was a bit confused about was that the URL you pointed us to earlier in this thread was working from the first time I visited it.

The 'norsrc' error will not do.  Thanks for pointing that out. 

As for synbrowse, and synview, you may need to contact the authors directly, as I am not sure they monitor this list.

Sheldon

On Thu, Sep 3, 2009 at 12:10 AM, Wes Barris <wes.barris@...> wrote:

Sheldon McKay wrote:

Hi Wes,

The URL you provided was working when I checked it.  A CVS update
should silence the annoying but harmless 'shellwords' squawks.  The
'Use of uninitialized value in hash element at
/usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006'
error is a symptom of specifying a search source (species) that does
not exist in the configuration file.  I added a sanity check here so
that a warning will be thrown when a specified data source is not
known or configured.

Thanks Sheldon.  A CVS update has stopped the apache error messages from
occurring.  Also, as you state, gbrowse_syn is working.

The initial display of gbrowse_syn contains an error "Species 'nosrc'
is not configured for this database" and doesn't show a synteny
alignment until one selects an example region.  This led me to believe
that it wasn't working.

I had just finished trying to get both synbrowse and synview working.
When both of those failed I guess that I was just expecting gbrowse_syn
to fail too.

Sheldon


On Fri, Aug 28, 2009 at 12:23 AM, Wes Barris<wes.barris@...> wrote:

Sheldon McKay wrote:

Just to confirm, you are running Gbrowse 1.7?

Ok.  I have recovered from the Bio-Graphics-1.982 install.  I have
edited all of my other .conf files so that there are no errors reported
in the apache log file when viewing normal gbrowse databases.

Now, back to gbrowse_syn.  When gbrowse_syn is used to view the
oryza database, these errors are logged by apache:

[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217] Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 67,
<DATA> line 192.
[Fri Aug 28 14:17:29 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 14:17:31 2009] [error] [client 140.253.153.217] [Fri Aug 28
14:17:31 2009] gbrowse_syn.cgi: Use of uninitialized value in hash element
at /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/FeatureFile.pm line 1006.

I don't receive the "shellwords" errors with viewing gbrowse
databases.

The URL that can be used to see the results is:

http://www.livestockgenomics.csiro.au/perl/gbrowse_syn.cgi/oryza/

I have the absolute latest versions of bioperl, gbrowse, biographics
and any dependencies required by bioperl.

The only differences between the provided .conf files and what I am
running has to do with the location of the database server:

wes@bioactive> diff
/usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/oryza.synconf
oryza.synconf
5c5
< join        = dbi:mysql:database=rice_synteny;host=localhost;user=nobody
---

join        =
dbi:mysql:database=rice_synteny;host=biodata.sl.csiro.au;user=nobody

wes@bioactive> diff
/usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/rice.conf
rice.conf
5c5
<                      -dsn     dbi:mysql:rice;host=localhost
---

                    -dsn     dbi:mysql:rice;host=biodata.sl.csiro.au

wes@bioactive> diff
/usr/local/src/bioinformatics/gbrowse/gbrowse_syn/rice/conf/wild_rice.conf
wild_rice.conf
5c5
<                      -dsn     dbi:mysql:wild_rice;host=localhost
---

                    -dsn     dbi:mysql:wild_rice;host=biodata.sl.csiro.au

Sheldon

On Thu, Aug 27, 2009 at 9:15 PM, Wes Barris<wes.barris@...> wrote:

Sheldon McKay wrote:

Can't hurt!

I just installed Bio-Graphics-1.982 from CPAN and now everything
is broke.  I can no longer even view a regular gbrowse database.
I'll try some older versions of Bio-Graphics and see if I can
get our site up and running again.

On Thu, Aug 27, 2009 at 8:59 PM, Wes Barris<wes.barris@...> wrote:

Sheldon McKay wrote:

Hi Wes,

The shellwords error messages are not related, I think.  One more
question I forgot to ask: did you update Bio::Graphics from CPAN?

No, I didn't.  Should I?

Sheldon

On Thu, Aug 27, 2009 at 8:45 PM, Wes Barris<wes.barris@...>
wrote:

Sheldon McKay wrote:

Hi Wes,

It looks like it might have something to to with the configuration
file.  Could you update your bioperl to a new svn checkout of
bioperl-live
and also have you changed the configuration files at all?

Hi Sheldon,

I updated bioperl using the latest svn checkout.  This required me
to update several perl modules as well.  Now I'm completely
up-to-date.

I'm not seeing any difference in gbrowse_syn.  I'm getting these
errors in my apache error log file:

[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]
Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
67,
<DATA> line 192.
[Fri Aug 28 10:41:23 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]
Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
67,
<DATA> line 192.
[Fri Aug 28 10:41:26 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Fri Aug 28 10:41:28 2009] [error] [client 140.253.153.217] [Fri Aug
28
10:41:28 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
element
at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
line 806.

The only change that I have made to the three .conf files is to
change the -dsn args from "localhost" to the name of our database
server which runs mysql.

Sheldon

On Wed, Aug 26, 2009 at 9:55 PM, Wes Barris<wes.barris@...>
wrote:

Hi,

I have followed the excellent Gbrowse_syn tutorial
http://gmod.org/wiki/GBrowse_syn_Tutorial in an attempt to get
a working local copy of the sample rice/wild_rice synteny browser
working.  I have successfully completed all steps.  However, the
final gbrowse_syn/oryza display does not display the overview
or synteny display.  The following errors are displayed in the
apache error log:

[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
Subroutine
Bio::Graphics::Browser::Synteny::shellwords redefined at
/usr/lib/perl5/5.8.5/Exporter.pm line 67, <DATA> line 192.
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at



/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Browser/Synteny.pm
line 11
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]
Subroutine
main::shellwords redefined at /usr/lib/perl5/5.8.5/Exporter.pm line
67,
<DATA> line 192.
[Thu Aug 27 11:24:45 2009] [error] [client 140.253.153.217]  at
/htdocs/gbrowse/gbrowse_syn.cgi line 27
[Thu Aug 27 11:24:47 2009] [error] [client 140.253.153.217] [Thu
Aug
27
11:24:47 2009] gbrowse_syn.cgi: Use of uninitialized value in hash
element
at




/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/FeatureFile.pm
line 806.

Do the above errors mean anything to anywone?

I have upgraded Exporter to the latest version (5.63).
I am running the latest gbrowse from CVS (downloaded yesterday).
I am running bioperl 1.6.

--
Wes Barris <wes.barris@...>





------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports
2008
30-Day
trial. Simplify your report design, integration and deployment -
and
focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Wes Barris <wes.barris@...>

--
Wes Barris <wes.barris@...>

--
Wes Barris <wes.barris@...>

--
Wes Barris <wes.barris@...>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States

--

Wes Barris <wes.barris@...>

--

Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, Connecticut, United States

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]


------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse