[Gmod-gbrowse] 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/
<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

[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

Post by 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/
<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: [phone]www.ccamp.res.in/NGS-Genomics
------------------------------------------------------------------------------
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[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

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

Post by 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

Post by 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/
<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: [phone]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
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: [phone]www.ccamp.res.in/NGS-Genomics