problem with GBrowse2 search

[陈冠华]

Hi,

I am moving from GBrowse1.69 to GBrowse 2. The .gff works fine for GBrowse 1.69, so I think .conf is the problem. For GBrowse.conf I keep it as installation(except add my directory for my own project), for the project.conf file it is as follows(it is for displaying human genome data):
[GENERAL]
description   = annoproject
database      = annoproject      
default tracks = GAD:region
initial landmark = chr1:143000..180000
default width = 800
automatic classes = chromosome cytoband gene
[annoproject:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /var/www/html/gbrowse2/databases/annoproject
# OMIM the [TRACK DEFAULT] and [TRACK]
When I search "chr1" --- it returns "20 matches",but no graph display. When I search "chr1:100000..110000"--- it returns"landmark is not recognized". I wonder if I miss any thing in the .conf file. The attachement have pictures that show what the error is.



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[Scott Cain-4]

Several questions:

- What build of GBrowse 2 is this?  And what version of Bio::Graphics?

- Are there any messages in the appache error_log?

- Does the "20 matches" message make sense for  your data?  If not, do
you have any ideas why it might be saying there are 20 matches?

Scott


On Thu, Jun 4, 2009 at 9:02 AM, 陈冠华 <cghhust@...> wrote:

> Hi,
>
> I am moving from GBrowse1.69 to GBrowse 2. The .gff works fine for GBrowse
> 1.69, so I think .conf is the problem. For GBrowse.conf I keep it as
> installation(except add my directory for my own project), for the
> project.conf file it is as follows(it is for displaying human genome data):
> [GENERAL]
> description   = annoproject
> database      = annoproject
> default tracks = GAD:region
> initial landmark = chr1:143000..180000
> default width = 800
> automatic classes = chromosome cytoband gene
> [annoproject:database]
> db_adaptor    = Bio::DB::SeqFeature::Store
> db_args       = -adaptor memory
>                 -dir    /var/www/html/gbrowse2/databases/annoproject
> # OMIM the [TRACK DEFAULT] and [TRACK]
> When I search "chr1" --- it returns "20 matches",but no graph display. When
> I search "chr1:100000..110000"--- it returns"landmark is not recognized". I
> wonder if I miss any thing in the .conf file. The attachement have pictures
> that show what the error is.
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
> Go to: http://p.sf.net/sfu/opensolaris-get
> _______________________________________________
> 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

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse