Re: [Gmod-ajax] JBrowse 2 setup: jbrowse command fails

[Vaneet L. <van...@uc...>]

Thanks Colin, that was the issue.  I’ve upgraded to Node v20.  I only stuck with my current version as the JBrowse instructions mentioned that Node v12+ was fine.

Thank you,

Vaneet

From: Colin <col...@gm...>
Sent: September 26, 2023 4:01 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse 2 setup: jbrowse command fails

[△EXTERNAL]

Can you check what version of "node" you have? Run

node --version

We recommend you get the latest node.js e.g. v20

There are multiple options for installing nodejs but one option is for example listed here https://github.com/nodesource/distributions#installation-instructions

-Colin



On Tue, Sep 26, 2023 at 4:17 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

I’ve just begun to start setting up and installing JBrowse 2.  I thought I had installed it properly but I notice now that my jbrowse command fails every time it’s run with Syntax Errors, no matter which sub-command I use.  Here are some examples:

jbrowse create jbrowse2

SyntaxError: Unexpected token '.'

jbrowse upgrade

SyntaxError: Unexpected token '('

jbrowse add-assembly genome.fa --load copy --out /var/www/html/jbrowse/

SyntaxError: Unexpected token '.'

For adding the assembly I used the actual URL of my genome fasta file after the indexes were created with samtools.  I got around the first command failing by manually downloading and placing the newest edition of JBrowse2 in my desired directory.  However using the ‘jbrowse’ command is obviously fundamental to operating JBrowse2 and adding tracks and genomes, so I need that to work.  Not sure if something in the underlying JBrowse2 code is causing this error.

Thanks,

Vaneet

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

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