|

Scientific/Engineering

»

Bio-Informatics

»

Generic Model Organism System Database

»

GBrowse 2: no graph show after search

View: New views

5 Messages — Rating Filter: Alert me

	GBrowse 2: no graph show after search by 陈冠华 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi, After I search any content in the search bar(chr1), match found but no graph display. Do anyone know why this happens? When I search (chr1:100000..110000), it returns "The landmark named chr1:100000..110000 is not recognized" My annoproject.conf file is as follows: [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 [TRACK DEFAULTS] glyph = generic database = annoproject height = 8 bgcolor = black fgcolor = black label density = 50 bump density = 100 [CYT:overview] feature = chromosome glyph = ideogram fgcolor = black bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray gpos75:darkgray gpos100:black acen:cen gvar:var arcradius = 6 height = 25 bump = 0 label = 0 key = Ideogram [GAD] database = annoproject feature = gene:gad glyph = generic stranded = 1 bgcolor = grey fgcolor = black height = 10 key = GAD category = gene description = 0 I made no change to GBrowse.conf except add these two lines: [annoproject] description = annoproject path = annoproject.conf Attachment also include the data file. Thank you very much! Yours Josh ------------------------------------------------------------------------------ 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 2.jpg (256K) Download Attachment 4.jpg (205K) Download Attachment cytoBand.gff (125K) Download Attachment gad.gff (341K) Download Attachment
	GBrowse 2: no graph show after search by 陈冠华 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi, After I search any content in the search bar(chr1), match found but no graph display. Do anyone know why this happens? When I search (chr1:100000..110000), it returns "The landmark named chr1:100000..110000 is not recognized" My annoproject.conf file is as follows: [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 [TRACK DEFAULTS] glyph = generic database = annoproject height = 8 bgcolor = black fgcolor = black label density = 50 bump density = 100 [CYT:overview] feature = chromosome glyph = ideogram fgcolor = black bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray gpos75:darkgray gpos100:black acen:cen gvar:var arcradius = 6 height = 25 bump = 0 label = 0 key = Ideogram [GAD] database = annoproject feature = gene:gad glyph = generic stranded = 1 bgcolor = grey fgcolor = black height = 10 key = GAD category = gene description = 0 I made no change to GBrowse.conf except add these two lines: [annoproject] description = annoproject path = annoproject.conf Attachment also include the data file. Thank you very much! Yours Josh ------------------------------------------------------------------------------ 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
	GBrowse 2: no graph show after search by 陈冠华 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi, After I search any content in the search bar(chr1), match found but no graph display. Do anyone know why this happens? When I search (chr1:100000..110000), it returns "The landmark named chr1:100000..110000 is not recognized" My annoproject.conf file is as follows: [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 [TRACK DEFAULTS] glyph = generic database = annoproject height = 8 bgcolor = black fgcolor = black label density = 50 bump density = 100 [CYT:overview] feature = chromosome glyph = ideogram fgcolor = black bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray gpos75:darkgray gpos100:black acen:cen gvar:var arcradius = 6 height = 25 bump = 0 label = 0 key = Ideogram [GAD] database = annoproject feature = gene:gad glyph = generic stranded = 1 bgcolor = grey fgcolor = black height = 10 key = GAD category = gene description = 0 I made no change to GBrowse.conf except add these two lines: [annoproject] description = annoproject path = annoproject.conf Attachment also include the data file. Thank you very much! Yours Josh ------------------------------------------------------------------------------ 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
	GBrowse 2: no graph show after search by 陈冠华 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi, After I search any content in the search bar(chr1), match found but no graph display. Do anyone know why this happens? When I search (chr1:100000..110000), it returns "The landmark named chr1:100000..110000 is not recognized" My annoproject.conf file is as follows: [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 [TRACK DEFAULTS] glyph = generic database = annoproject height = 8 bgcolor = black fgcolor = black label density = 50 bump density = 100 [CYT:overview] feature = chromosome glyph = ideogram fgcolor = black bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray gpos75:darkgray gpos100:black acen:cen gvar:var arcradius = 6 height = 25 bump = 0 label = 0 key = Ideogram [GAD] database = annoproject feature = gene:gad glyph = generic stranded = 1 bgcolor = grey fgcolor = black height = 10 key = GAD category = gene description = 0 I made no change to GBrowse.conf except add these two lines: [annoproject] description = annoproject path = annoproject.conf Attachment also include the data file. Thank you very much! Yours Josh ------------------------------------------------------------------------------ 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
	Re: GBrowse 2: no graph show after search by Lincoln Stein-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message I don't think anyone understands what it is you are asking. Could you post a screenshot? Lincoln On Wed, Jun 3, 2009 at 1:28 PM, 陈冠华 <cghhust@...> wrote: Hi, After I search any content in the search bar(chr1), match found but no graph display. Do anyone know why this happens? When I search (chr1:100000..110000), it returns "The landmark named chr1:100000..110000 is not recognized" My annoproject.conf file is as follows: [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 [TRACK DEFAULTS] glyph = generic database = annoproject height = 8 bgcolor = black fgcolor = black label density = 50 bump density = 100 [CYT:overview] feature = chromosome glyph = ideogram fgcolor = black bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray gpos75:darkgray gpos100:black acen:cen gvar:var arcradius = 6 height = 25 bump = 0 label = 0 key = Ideogram [GAD] database = annoproject feature = gene:gad glyph = generic stranded = 1 bgcolor = grey fgcolor = black height = 10 key = GAD category = gene description = 0 I made no change to GBrowse.conf except add these two lines: [annoproject] description = annoproject path = annoproject.conf Attachment also include the data file. Thank you very much! Yours Josh ------------------------------------------------------------------------------ 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 -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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