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Command line tools

This document covers the CLI tools. Note: for @jbrowse/img static export tool, see https://www.npmjs.com/package/@jbrowse/img

Note: the @jbrowse/cli may not do all types of operations, some use cases may best be handled by creating your own tools to manipulate a config.json by hand or by using a script file.

A simple script that does not use @jbrowse/cli at all may just look like this

const config = JSON.parse(fs.readFileSync('config.json', 'utf8'))
// do something with config.tracks, config.assemblies, etc.
fs.writeFileSync('config.json', JSON.stringify(config, null, 2))

Installation​

The command line tools can be installed globally using npm as follows

$ npm install -g @jbrowse/cli

A CLI tool called jbrowse should then be available in the path. You can test your installation with

$ jbrowse --version

It is also possible to do one-off executions using npx, e.g.

npx @jbrowse/cli create myfolder

It is likely preferable in most cases to install the tools globally with npm install @jbrowse/cli -g however

jbrowse create​

jbrowse add-assembly​

jbrowse add-track​

jbrowse text-index​

jbrowse admin-server​

jbrowse upgrade​

jbrowse make-pif​

jbrowse sort-gff​

jbrowse sort-bed​

jbrowse add-connection​

jbrowse add-track-json​

jbrowse remove-track​

jbrowse set-default-session​