Re: [Gmod-ajax] JBrowse2 config.json

[Ke J. <bio...@gm...>]

Sounds good! These are very valuable comments. Thanks!

On Tue, Nov 17, 2020 at 11:03 AM Colin <col...@gm...> wrote:

> In general we do allow and encourage putting multiple genome assemblies in
> a single config.json.for jbrowse 2. Then each track specifies which
> assembly each track belongs to (or for synteny tracks, which assemblies
> [plural] it belongs to)
>
>
>
> In Jbrowse 2 we allow ?config= so you could have multiple unrelated
> configs but we have not made the "include" system of jbrowse 1 that lets
> you merge multiple configs though.
>
> If this is seems important to separate things out, let us know but single
> config.json containing multiple assemblies is the current concept :)
>
> -Colin
>
> On Mon, Nov 16, 2020, 10:28 AM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I've been playing with JBrowse2 first release for a few days. In
>> JBorwse (1), I've been using a strategy to separate configuration and data
>> for multiple genomes by creating config.json for each genome (and pointing
>> data to the corresponding genomic data). It worked pretty well as it
>> reduced chances of messing up other genomes while making changes to one
>> genome. I noticed for JBrowse2, there is a master config.json sitting in
>> the JBrowe2 folder and we lay out multiple genomes and assemblies in it. Is
>> this the way to manage multiple genomes in JBrowse2 now? Because JBrowse2
>> has to consider the multiple genome view for synteny, so everything has to
>> be in one single config.json? Or more generally, what is the general idea
>> (or best practices?) of handling multiple organisms in JBrowse2?
>>
>> Thanks again for the development of JBrowse 2! It is truly exciting to
>> see it!
>>
>> Ke
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>