Having difficulty adding .delta files as synteny tracks through the command line

[carolyncaron]

Hello,

I have 10+ .delta files generated using nucmer that I want to add as synteny tracks (and many more files are coming). I updated my JBrowse2 version to v2.4.2 since I noticed that v2.4.1 mentions adding functionality for adding synteny tracks through the CLI, but I am getting errors.

Here is what I've tried based on commands in the docs:

jbrowse add-track 1GRN-1DRT.delta --type SyntenyTrack --assemblyNames Lcu.1GRN,Ler.1DRT --load symlink
›   Error: Unexpected arguments: --type, SyntenyTrack
›   See more help with --help

jbrowse add-track 1GRN-1DRT.delta --assemblyNames Lcu.1GRN,Ler.1DRT --load symlink
 ›   Error: Track type is not recognized

I tried adding the same delta file through the user interface and it works. It also works by updating the config.json directly - but I'd really like to avoid doing it this way for all of them!

Is there a parameter in the command that I'm missing? Any suggestions for how to get this to work?

[cmdcolin]

One thing that may be of note is that you would want your CLI tools to be up to date. The version of 'jbrowse-web' (what you see in the browser) can be different from the version of the 'CLI tool' (what the jbrowse command is)

to update the CLI tools (the jbrowse command), can use

npm install -g @jbrowse/cli

Then run

jbrowse --version

To confirm the CLI tool version

[cmdcolin]

I can run similar command with the latest version (add a delta file) and I think it should work. I am hoping to write some more tutorials on loading different types of synteny data soon, as we have only really documented minimap2/PAF file loading somewhat, but the CLI tool should support delta after you get it updated. Example command I see locally

$ jbrowse add-track volvox_inv_indels.delta --out test --assemblyNames volvox,volvox_inv --load symlink

Added track with name "volvox_inv_indels" and trackId "volvox_inv_indels" to test/config.json

[cmdcolin]

and just as another note, if you see e.g. the data is empty after loading, can try switching the order of --assemblyNames you pass in

[carolyncaron]

Thanks so much for your quick reply! My CLI tool was indeed out of date so updating it allowed me to run the second command I tried successfully. 👍

[rbuels]

I'm wondering @cmdcolin if it would be worth having the CLI tool check whether it is out of date and give a warning if so? yarn does this I think.

[cmdcolin]

could make an issue for it. the CLI is a pretty slow moving target and may not need frequent updates, but occasionally updating can help e.g. in things like this