[Gmod-gbrowse] New Dataset for GBrowse not working

[Andy Pham]

Hi,
I just finished loading loading a dataset into a postgres sql database
using:
bp_seqfeature_load -c -d 'dbname=gb_maes_publicgenomev4_g_gff3;host=****'
-a 'DBI::Pg' -u **** -p **** Maes.gff3

However, when I try to open the URL to see the gbrowse for this particular
dataset, it redirects to another dataset. I've tried restarting the apache
service and triple checking the names of both the database and the config
files to see if they match up.

The GBrowse.config has this in it:

[maes_genomev4]
description = M.esculenta (Cassava) Genome v4.1
path = maes.conf

The maes.conf file is attached. Previous datasets have successfully loaded
before but for some reason this dataset is giving us problems. I have also
checked the sql database and there is data in that database, so the gff3
file loaded successfully. The permissions for the files have been checked
as well. The server just doesn't seem to see the changes in the config
files.

[Scott Cain]

Hi Andy,

While I don't see anything obviously wrong with you configuration file, the
redirecting to another data set is a symptom of there being something wrong
with the config. The redirecting is sort of like GBrowse saying, "I can't
do that, maybe this will help" even though it never really does :-/

Is there anything in the apache error log that might give a hint at what
the problem is? If not, I'd suggest trimming things out that are
unnecessary like include files and the tooltip section. Also, make sure
that the connection info for the database is correct and that the apache
user can connect to the database.

Scott

Post by Andy Pham
Hi,
I just finished loading loading a dataset into a postgres sql database
bp_seqfeature_load -c -d 'dbname=gb_maes_publicgenomev4_g_gff3;host=****'
-a 'DBI::Pg' -u **** -p **** Maes.gff3
However, when I try to open the URL to see the gbrowse for this particular
dataset, it redirects to another dataset. I've tried restarting the apache
service and triple checking the names of both the database and the config
files to see if they match up.
[maes_genomev4]
description = M.esculenta (Cassava) Genome v4.1
path = maes.conf
The maes.conf file is attached. Previous datasets have successfully loaded
before but for some reason this dataset is giving us problems. I have also
checked the sql database and there is data in that database, so the gff3
file loaded successfully. The permissions for the files have been checked
as well. The server just doesn't seem to see the changes in the config
files.
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[Andy Pham]

Hi,
Thanks for the response! The apache error log shows no errors, just that it
tries to connect to maes_genomev4, and the redirect to something it can
find. No errors being recorded. The apache user and password are working
correctly, and the connection info is correct as well. I did trim out the
include files and tooltip section, but it's still redirecting as usual.
Thanks,
Andy

Post by Scott Cain
Hi Andy,
While I don't see anything obviously wrong with you configuration file,
the redirecting to another data set is a symptom of there being something
wrong with the config. The redirecting is sort of like GBrowse saying, "I
can't do that, maybe this will help" even though it never really does :-/
Is there anything in the apache error log that might give a hint at what
the problem is? If not, I'd suggest trimming things out that are
unnecessary like include files and the tooltip section. Also, make sure
that the connection info for the database is correct and that the apache
user can connect to the database.
Scott

Post by Andy Pham
Hi,
I just finished loading loading a dataset into a postgres sql database
bp_seqfeature_load -c -d 'dbname=gb_maes_publicgenomev4_g_gff3;host=****'
-a 'DBI::Pg' -u **** -p **** Maes.gff3
However, when I try to open the URL to see the gbrowse for this
particular dataset, it redirects to another dataset. I've tried restarting
the apache service and triple checking the names of both the database and
the config files to see if they match up.
[maes_genomev4]
description = M.esculenta (Cassava) Genome v4.1
path = maes.conf
The maes.conf file is attached. Previous datasets have successfully
loaded before but for some reason this dataset is giving us problems. I
have also checked the sql database and there is data in that database, so
the gff3 file loaded successfully. The permissions for the files have been
checked as well. The server just doesn't seem to see the changes in the
config files.
------------------------------------------------------------------------------
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