Problem with running Volvox

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Problem with running Volvox

Ashwini M
Hi,

I have installed gbrowse successfully. Following the tutorial I started with volvox database. After all the steps when I go to https://localhost/cgi-bin/gb2/gbrowse/volvox/ it says

Can't call method "get_feature_by_name" on an undefined value.

Could you please let me know why this could be happening.

I will be happy to provide any other information.

Regards,
Ashwini M

--
Ashwini M
Next-Generation Genomics Laboratory
Centre for Cellular and Molecular Platform
National Centre for Biological Sciences
Bangalore BioCluster, NCBS-GKVK Campus
Bangalore 560065, India
Lab Phone:    91-080-67185105
www.ccamp.res.in/NGS-Genomics

------------------------------------------------------------------------------
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Performance metrics, stats and reports that give you Actionable Insights
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Re: Problem with running Volvox

Scott Cain
Hi Ashwini,

It could be several things.  Is there any more detail in the apache error log that might shed light on why it's happening?  Perhaps the database directory isn't accessible to the webserver so it isn't able to read the GFF files, or the configuration file has the wrong directory for the database directory.

Scott


On Fri, May 22, 2015 at 1:40 AM, Ashwini M <[hidden email]> wrote:
Hi,

I have installed gbrowse successfully. Following the tutorial I started with volvox database. After all the steps when I go to https://localhost/cgi-bin/gb2/gbrowse/volvox/ it says

Can't call method "get_feature_by_name" on an undefined value.

Could you please let me know why this could be happening.

I will be happy to provide any other information.

Regards,
Ashwini M

--
Ashwini M
Next-Generation Genomics Laboratory
Centre for Cellular and Molecular Platform
National Centre for Biological Sciences
Bangalore BioCluster, NCBS-GKVK Campus
Bangalore 560065, India
Lab Phone:    91-080-67185105
www.ccamp.res.in/NGS-Genomics

------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
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Re: Problem with running Volvox

Ashwini M
Hi Scott,

Yes, the configuration file was pointing to wrong directory "/var/www/gbrowse2". I changed it and it was all working fine. But when I try after few days it is giving the same error. I have attached the screenshots for your reference. Please let me know if you need further information in understanding why this problem could be occurring.

Regards,
Ashwini M


On Fri, May 22, 2015 at 9:09 PM, Scott Cain <[hidden email]> wrote:
Hi Ashwini,

It could be several things.  Is there any more detail in the apache error log that might shed light on why it's happening?  Perhaps the database directory isn't accessible to the webserver so it isn't able to read the GFF files, or the configuration file has the wrong directory for the database directory.

Scott


On Fri, May 22, 2015 at 1:40 AM, Ashwini M <[hidden email]> wrote:
Hi,

I have installed gbrowse successfully. Following the tutorial I started with volvox database. After all the steps when I go to https://localhost/cgi-bin/gb2/gbrowse/volvox/ it says

Can't call method "get_feature_by_name" on an undefined value.

Could you please let me know why this could be happening.

I will be happy to provide any other information.

Regards,
Ashwini M

--
Ashwini M
Next-Generation Genomics Laboratory
Centre for Cellular and Molecular Platform
National Centre for Biological Sciences
Bangalore BioCluster, NCBS-GKVK Campus
Bangalore 560065, India
Lab Phone:    91-080-67185105
www.ccamp.res.in/NGS-Genomics

------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




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



--
Ashwini M
Next-Generation Genomics Laboratory
Centre for Cellular and Molecular Platform
National Centre for Biological Sciences
Bangalore BioCluster, NCBS-GKVK Campus
Bangalore 560065, India
Lab Phone:    91-080-67185105
www.ccamp.res.in/NGS-Genomics

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

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Re: Problem with running Volvox

Scott Cain
Hi Ashwini,

Something went wrong during the installation, since the "$PERSISTENT" should have be replaced with a real file path when the configuration was installed.  Did you run "perl Build.PL; ./Build; sudo ./Build install"?  You can either try to reinstall, paying attention to any errors the installer emits, or look for any instances of $PERSISTENT and replace them with what should be there.

Scott


On Wed, Jul 29, 2015 at 8:11 AM, Ashwini M <[hidden email]> wrote:
Hi Scott,

Yes, the configuration file was pointing to wrong directory "/var/www/gbrowse2". I changed it and it was all working fine. But when I try after few days it is giving the same error. I have attached the screenshots for your reference. Please let me know if you need further information in understanding why this problem could be occurring.

Regards,
Ashwini M


On Fri, May 22, 2015 at 9:09 PM, Scott Cain <[hidden email]> wrote:
Hi Ashwini,

It could be several things.  Is there any more detail in the apache error log that might shed light on why it's happening?  Perhaps the database directory isn't accessible to the webserver so it isn't able to read the GFF files, or the configuration file has the wrong directory for the database directory.

Scott


On Fri, May 22, 2015 at 1:40 AM, Ashwini M <[hidden email]> wrote:
Hi,

I have installed gbrowse successfully. Following the tutorial I started with volvox database. After all the steps when I go to https://localhost/cgi-bin/gb2/gbrowse/volvox/ it says

Can't call method "get_feature_by_name" on an undefined value.

Could you please let me know why this could be happening.

I will be happy to provide any other information.

Regards,
Ashwini M

--
Ashwini M
Next-Generation Genomics Laboratory
Centre for Cellular and Molecular Platform
National Centre for Biological Sciences
Bangalore BioCluster, NCBS-GKVK Campus
Bangalore 560065, India
Lab Phone:    91-080-67185105
www.ccamp.res.in/NGS-Genomics

------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Ashwini M
Next-Generation Genomics Laboratory
Centre for Cellular and Molecular Platform
National Centre for Biological Sciences
Bangalore BioCluster, NCBS-GKVK Campus
Bangalore 560065, India
Lab Phone:    91-080-67185105
www.ccamp.res.in/NGS-Genomics



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

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