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GBrowse_syn doesn't display Aligned species and Display mode.

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	GBrowse_syn doesn't display Aligned species and Display mode. by Rytsareva, Inna (I) :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message GBrowse_syn doesn’t display Aligned species and Display mode. I'm trying to set up Gbrowse_syn for WormBase. In the "Search" section I cannt see sections "Aligned species" and "Display mode". I have only syn and confsyn files from an sample dataset. Inna Rytsareva Discovery Information Management Dow AgroSciences Indianapolis, IN 317-337-4716 ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: GBrowse_syn doesn't display Aligned species and Display mode. by Sheldon McKay-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Inna, Based on the limited information you have given, I am guessing maybe you only have two species, in which case those two user interface features do not appear because they are not necessary. However for more help, please provide much more detailed feedback, URL, screenshots, conf files, data, etc, etc, so we can better help you. Sheldon On Tue, Jun 9, 2009 at 1:27 PM, Rytsareva, Inna (I) <IRytsareva@...> wrote: I'm trying to set up Gbrowse_syn for WormBase. In the "Search" section I cannt see sections "Aligned species" and "Display mode". I have only syn and confsyn files from an sample dataset. Inna Rytsareva Discovery Information Management Dow AgroSciences Indianapolis, IN 317-337-4716 ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: GBrowse_syn doesn't display Aligned species and Display mode. by Sheldon McKay-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Inna, Please remeber to CC the list. You will need to upgrade to growse 1.7 (the latest stable version in cvs). If you use the netinstall script, re-run it with the -d option. Otherwise: install Bio::Graphics from CPAN update to the latest svn version of bioperl update to the latet cvs version fo gbrowse (-stable branch) Sheldon On Tue, Jun 9, 2009 at 2:44 PM, Rytsareva, Inna (I) <IRytsareva@...> wrote: Hello Sheldon. I'm trying to get a demo WormBase up and running. My screen looks like syn1.bmp. I have 5 species: c_brenneri, c_briggsae, c_elegans, c_remanei, c_japonica. There are .syn file for each species (like c_brenneri.syn) and pecan.synconf in a folder "gbrowse.conf", also gff files in a folder "gbrowse/databases" and an alignment database on Postgres. Inna Rytsareva* Discovery Information Management Dow AgroSciences Indianapolis, IN 317-337-4716 From: Sheldon McKay [mailto:sheldon.mckay@...] Sent: Tuesday, June 09, 2009 2:19 PM To: Rytsareva, Inna (I) Cc: gmod-gbrowse@... Subject: Re: [Gmod-gbrowse] GBrowse_syn doesn't display Aligned species and Display mode. Hi Inna, Based on the limited information you have given, I am guessing maybe you only have two species, in which case those two user interface features do not appear because they are not necessary. However for more help, please provide much more detailed feedback, URL, screenshots, conf files, data, etc, etc, so we can better help you. Sheldon On Tue, Jun 9, 2009 at 1:27 PM, Rytsareva, Inna (I) <IRytsareva@...> wrote: I'm trying to set up Gbrowse_syn for WormBase. In the "Search" section I cannt see sections "Aligned species" and "Display mode". I have only syn and confsyn files from an sample dataset. Inna Rytsareva Discovery Information Management Dow AgroSciences Indianapolis, IN 317-337-4716 ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: GBrowse_syn doesn't display Aligned species and Display mode. by ankita narang :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Sheldon , I have problem related to this thread, as i have taken 2 species as test for Gbrowse_syn but i am not able to visualise aligned display although i m getting the species genes dispaly indiviually as in Gbrowse, i have used the same config file as in wormbase but it cant display for 2 species will be the reason???? On Tue, Jun 9, 2009 at 11:48 PM, Sheldon McKay <sheldon.mckay@...> wrote: Hi Inna, Based on the limited information you have given, I am guessing maybe you only have two species, in which case those two user interface features do not appear because they are not necessary. However for more help, please provide much more detailed feedback, URL, screenshots, conf files, data, etc, etc, so we can better help you. Sheldon On Tue, Jun 9, 2009 at 1:27 PM, Rytsareva, Inna (I) <IRytsareva@...> wrote: I'm trying to set up Gbrowse_syn for WormBase. In the "Search" section I cannt see sections "Aligned species" and "Display mode". I have only syn and confsyn files from an sample dataset. Inna Rytsareva Discovery Information Management Dow AgroSciences Indianapolis, IN 317-337-4716 ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: GBrowse_syn doesn't display Aligned species and Display mode. by Sheldon McKay-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Please send data, your conf files, any screen shots etc, URLs etc. On Tue, Jun 9, 2009 at 3:03 PM, ankita narang <ankita.bioinfo77@...> wrote: Hi Sheldon , I have problem related to this thread, as i have taken 2 species as test for Gbrowse_syn but i am not able to visualise aligned display although i m getting the species genes dispaly indiviually as in Gbrowse, i have used the same config file as in wormbase but it cant display for 2 species will be the reason???? On Tue, Jun 9, 2009 at 11:48 PM, Sheldon McKay <sheldon.mckay@...> wrote: Hi Inna, Based on the limited information you have given, I am guessing maybe you only have two species, in which case those two user interface features do not appear because they are not necessary. However for more help, please provide much more detailed feedback, URL, screenshots, conf files, data, etc, etc, so we can better help you. Sheldon On Tue, Jun 9, 2009 at 1:27 PM, Rytsareva, Inna (I) <IRytsareva@...> wrote: I'm trying to set up Gbrowse_syn for WormBase. In the "Search" section I cannt see sections "Aligned species" and "Display mode". I have only syn and confsyn files from an sample dataset. Inna Rytsareva Discovery Information Management Dow AgroSciences Indianapolis, IN 317-337-4716 ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse