[Gmod-help] Re: [Gmod-gbrowse] gbrowse2 problem,please help

[陈冠华]

Hi,
The sample (yeast) database works good for me.However,myself not.Event
simplest database do not work(not coordinate show nor can not search).
For the general GBrowse.conf part.I only add lines:

[annoproject]
description  = annoproject
path         = annoproject.conf

For annoproject.conf content is :
[GENERAL]
description   = annoproject
database      = annoproject
default tracks = CYT:overview
default width = 800
automatic classes = chromosome Sequence
[annoproject:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /var/www/html/gbrowse2/databases/annoproject
cache_overview = 0
[TRACK DEFAULTS]
glyph       = generic
database = annoproject
height      = 8
bgcolor     = black
fgcolor     = black
label density = 50
bump density  = 100
[CYT:overview]
feature      = chromosome
glyph        = generic
stranded     = 1
bgcolor      = grey
fgcolor         = black
height       = 10

My .gff data is :

##gff-version 3
chr1    ensembl    chromosome    1    245522847    .    .    .
ID=chr1;Name=chr1
chr11    ensembl    chromosome    1    134452384    .    .    .
ID=chr11;Name=chr11
chr12    ensembl    chromosome    1    132449811    .    .    .
ID=chr12;Name=chr12

It still have error.
2009/6/11 Dave Clements, GMOD Help Desk <gmodhelp at googlemail.com>

> Hi Josh,
> The email below implies that you have a single .conf file.  If you are
> running GBrowse 2 you'll need a general .conf and an organism specific .conf
> file.  See http://gmod.org/wiki/GBrowse_2.0_HOWTO for more.  Please pay
> particular attention to the part on the GENERAL section.
> If you are running with two conf files, please include more of each in the
> email and indicate where one stops and the other starts.
> Thanks,
> Dave C.
>
> On Thu, Jun 11, 2009 at 12:36 PM, 陈冠华 <cghhust at gmail.com> wrote:
>
>> Hi,
>> GBrowse2 sample database(yeast) works fine on the server.However,myself
>> not.Event simplest database do not work(not coordinate show nor can not
>> search).
>> My .conf is:
>> [GENERAL]
>> description   = annoproject
>> database      = annoproject
>> default tracks = CYT:overview
>> default width = 800
>> automatic classes = chromosome Sequence
>> [annoproject:database]
>> db_adaptor    = Bio::DB::SeqFeature::Store
>> db_args       = -adaptor memory
>>                 -dir    /var/www/html/gbrowse2/databases/annoproject
>> cache_overview = 0
>> [TRACK DEFAULTS]
>> glyph       = generic
>> database = annoproject
>> height      = 8
>> bgcolor     = black
>> fgcolor     = black
>> label density = 50
>> bump density  = 100
>> [CYT:overview]
>> feature      = chromosome
>> glyph        = generic
>> stranded     = 1
>> bgcolor      = grey
>> fgcolor         = black
>> height       = 10
>>
>> .gff data is :
>> ##gff-version 3
>> chr1    ensembl    chromosome    1    245522847    .    .    .
>> ID=chr1;Name=chr1
>> chr11    ensembl    chromosome    1    134452384    .    .    .
>> ID=chr11;Name=chr11
>> chr12    ensembl    chromosome    1    132449811    .    .    .
>> ID=chr12;Name=chr12
>>
>> See the attachment picture for the detailed error!
>>
>> Yours
>> Josh
>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing
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>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
> --
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at:
>  AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration
>  Galaxy Workshop at NBIC: http://www.nbic.nl/nbic/newsevents/Galaxy/
>
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