DB not loading

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

DB not loading

David
Hello,

I'm having an issue getting started with gbrowse, any help would be appreciated.
I have the yeast-simple example running successfully, and am working on a simple custom DB.

Things I have done:

I copied the volvox.conf file to bedbug_orco.conf in /etc/gbrowse/, and modified the -dir db_arg to point at '/var/lib/gbrowse/databases/bedbug_scaffold26' (db_adaptor is Bio::DB::SeqFeature::Store".  I changed the 'ctgA' references to 'Scaffold26'.

In the bedbug_scaffold26 directory I have a gff3 file called scaff26.gff3 which contains:
"##gff-version 3
##Index-subfeatures 1

Scaffold26    .    chromosome    1    65548    .    .    .    ID=Scaffold26;Name=Scaffold26"

I also have a file called scaffold26.fa, which contains one fasta entry:
">Scaffold26
sequence..."

I've edited GBrowse.conf and added:
[bedbug]
description   = Bedbug Scaffold26
path          = bedbug_orco.conf

What happens:

When I navigate to "localhost/cgi-bin/gbrowse/gbrowse/bedbug/" I get, underneath file/help:
"Bedbug Scaffold 26: 0bp from :.."
Landmark or region is set to "Scaffold26",  "Examples: Scaffold26"
"Data Source: Bedbug Scaffold26"

If I change the landmark or region to something like "Scaffold26:500..5000" I get "Not Found" under the file/help menus in red text.

Thanks,
David

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel
Reply | Threaded
Open this post in threaded view
|

Re: DB not loading

Scott Cain
Hi David,

I'm cc'ing this to the GBrowse list.  Future replies can trim off the gmod-devel list.

It looks to me like you've done everything you need to do.  The only thing I can think of is whether the bedbug database directory is writable by the webserver.  Also, did you get anything more helpful in the apache error_log?

Scott



On Fri, Apr 5, 2013 at 6:12 PM, David Price <[hidden email]> wrote:
Hello,

I'm having an issue getting started with gbrowse, any help would be appreciated.
I have the yeast-simple example running successfully, and am working on a simple custom DB.

Things I have done:

I copied the volvox.conf file to bedbug_orco.conf in /etc/gbrowse/, and modified the -dir db_arg to point at '/var/lib/gbrowse/databases/bedbug_scaffold26' (db_adaptor is Bio::DB::SeqFeature::Store".  I changed the 'ctgA' references to 'Scaffold26'.

In the bedbug_scaffold26 directory I have a gff3 file called scaff26.gff3 which contains:
"##gff-version 3
##Index-subfeatures 1

Scaffold26    .    chromosome    1    65548    .    .    .    ID=Scaffold26;Name=Scaffold26"

I also have a file called scaffold26.fa, which contains one fasta entry:
">Scaffold26
sequence..."

I've edited GBrowse.conf and added:
[bedbug]
description   = Bedbug Scaffold26
path          = bedbug_orco.conf

What happens:

When I navigate to "localhost/cgi-bin/gbrowse/gbrowse/bedbug/" I get, underneath file/help:
"Bedbug Scaffold 26: 0bp from :.."
Landmark or region is set to "Scaffold26",  "Examples: Scaffold26"
"Data Source: Bedbug Scaffold26"

If I change the landmark or region to something like "Scaffold26:500..5000" I get "Not Found" under the file/help menus in red text.

Thanks,
David

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel




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

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel