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Re: [Gmod-ajax] A question for JBrowse1
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From: <fa...@ca...> - 2022-03-27 08:46:24
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Thanks very much. We have tested view->trackPadding, yes, it works now! fa...@ca... From: Colin Date: 2022-03-26 00:15 To: Scott Cain CC: Ian Holmes; fa...@ca...; gmod-ajax Subject: Re: [Gmod-ajax] A question for JBrowse1 >However, we met a problem on setting the distance between each tracks. You can try setting view->trackPadding (see https://jbrowse.org/docs/global_options.html) Basically, editing jbrowse.conf to have [GENERAL] view.trackPadding=0 -Colin On Thu, Mar 24, 2022 at 3:08 PM Scott Cain <sc...@sc...> wrote: Hi Wei, While I agree with Ian's suggestion that you try JBrowse 2, if there is a reason you want to stick with JBrowse 1 for the moment, note that there is at least an option to add a little bit of space between tracks so that the labels don't overlap the features by adding "trackLabels = no-block" to the "[GENERAL]" section of the jbrowse.conf file for the entire site. Scott On Thu, Mar 24, 2022 at 1:48 PM Ian Holmes <ihh...@gm...> wrote: Dear Wei, Thanks for your interest in JBrowse. I'm glad it's been helpful to you! JBrowse1, which is now in maintenance mode only, does not allow adjustment of the vertical height of tracks. Active development of JBrowse is now focused on JBrowse2, whose "Linear Genome Browser" component reproduces most of the functionality of JBrowse1, while fixing a lot of the limitations. For example, it is easy to adjust the height of tracks in JBrowse2. There are also many new features, such as the ability to view synteny between genomes. Furthermore, JBrowse2 should be straightforward to install on any website where you already have JBrowse1 installed. We would be very interested in hearing feedback on your experience with JBrowse2, as we are actively encouraging new users to try JBrowse2, and would like to try and make the experience as easy as possible for you. I have CC'd the JBrowse mailing list on this reply; you can also often get quicker responses by engaging with the software development team directly in the various ways described on the contact page on the JBrowse website. Thanks & best wishes, Ian On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote: Dear Prof. Holmes, We are trying to build a genome website for our sequenced species, and found JBrowse1 an excellent tool to use. However, we met a problem on setting the distance between each tracks. Is there a way to set the distance of drawing among any neiboring tracks? Thanks for your great work. I am looking forward to hearing from you! Wei Fan Agriculture genomics Institute at Shenzhen, China fa...@ca... _______________________________________________ Gmod-ajax mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-ajax -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) _______________________________________________ Gmod-ajax mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
