Cannot install jbrowse-1.16.11-release developer version on macos ventura

[thuynnguyen]

Hello,

I am having trouble installing the developer version of JBrowse 1 on my machine. I would like to use the developer version so that I can use plugins. Can you please help me troubleshoot?

Here is the information you need for my issue:

• JBrowse version: jbrowse-1.16.11-dev
• Web browser being used: Firefox
• Operating system if relevant: MacOS Ventura
• If it is setup related, setup.log (attached)

setup.log

Thank you, Thuy

[cmdcolin]

errors like this in your setup log

Size.c: loadable library and perl binaries are mismatched (got first handshake key 0xc700080, needed 0xfc00080)

have shown up before https://github.com/GMOD/jbrowse/issues/1624

I dunno the exact reason for it, if you think there are multiple versions of perl on your system e.g. homebrew or conda versions, may want to try to remove those at least while setting up jbrowse also. another tip was to run these commands

rm -rf ~/.cpanm
rm -rf extlib # extlib is a folder that is in the jbrowse directory
./setup.sh

but, even if you can't get this particular error with perl fixed, strictly speaking, you do not need the perl scripts to use jbrowse see https://jbrowse.org/docs/tutorial.html

this tutorial only uses indexed file formats and does not use any perl scripts. you can download files to your plugin folder and just run

node_modules/.bin/yarn build

this will compile the code, and then you can open up the index.html and see the results, and you won't need to run any perl scripts

note: you may need to downgrade your node.js version too. it says in setup.log that you are using 19 but currently jbrowse works with node.js 14 or less, see readme here https://github.com/GMOD/jbrowse