Re: [Gmod-ajax] A question for JBrowse1

[Colin <col...@gm...>]

>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
>> <https://jbrowse.org/jb2/>, 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
>> <https://jbrowse.org/jb2/contact/> 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...
>>>
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>>
>
>
> --
> ------------------------------------------------------------------------
> 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/)
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