Re: [Gmod-ajax] JBrowse2 config file

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Thanks for that great info!

I find it cleaner having different config files but if it loses the ability to compare multiple genomes at once, I don’t think it’s worth it.  I’ll probably stick to one main config.json file.

Vaneet

From: Colin <col...@gm...>
Sent: April 8, 2025 1:00 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 config file

[△EXTERNAL]

Hi Vaneet
It will depend on your particular setup.

JBrowse 2 "likes" a single config.json, particularly because it enables comparing multiple genomes.

However, for either technical or administrative reasons, some people get overwhelmed by having a single config, and they make multiple configs

You can navigate to specific configs using

yoursite.com/jbrowse/?config=genomeA_config.json<http://yoursite.com/jbrowse/?config=genomeA_config.json>

You can also use the command line to write to specific configs using e.g.

jbrowse add-track --out genomeA_config.json

Finally, you can also optionally write scripts to merge configs. A script to merge configs tends to be pretty simple, you can simply concatenate the list of assemblies and tracks from different configs.

-Colin

PS We have had a couple great meetings with your XenBase colleagues!

On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I was curious when working with JBrowse2, is it very easy or user-friendly to setup multiple config.json files for the different genomes that may be hosted in the browser, similar to the original JBrowse?  If so, then please explain what the best way to do that is.  Or is JBrowse2 basically built to work best with one central config.json file as it is by default?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

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