This tool is used to find genes found in a location from Alliance Member JBrowse instances.

``
Usage: index [options]

_ ____ _ _ ____ _ _ _
| | __ ) _ __ _____ _____ ___ | \ | |/ ___| | (_)___| |_
_ | | _ \| '__/ _ \ \ /\ / / __|/ _ \ | \| | | | | | / __| __|
| |_| | |_) | | | (_) \ V V /\__ \ __/ | |\ | |___| |___| \__ \ |_
\___/|____/|_| \___/ \_/\_/ |___/\___| |_| \_|\____|_____|_|___/\__|

A wrapper around gmod/nclist-js. It returns JSON for generating cross references to JBrowse features

Options:
-V, --version output the version number
-b, --baseurl Path to JBrowse Data Directory - base URL for resolving relative URLs
-t, --template URL Template
-r, --refseq The Sequence name
-s, --start start position
-e, --end end position
-v, --verbose For debuging purposes
-h, --help display help for command
`

Requirements:
- node

Install node_modules

get the node_module dependencies

` bash
npm install
`

Compile CLI

create dist/index.js file to be run by node

`bash
npx tsc
`

Run the tool

`bash
node dist/index.js --help
`


Example command:
`
node dist/index.js -b "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS286/c_elegans_PRJNA13758/" -t "tracks/Curated_Genes/{refseq}/trackData.jsonz" -s 5692675 -e 5692315 -r III
`

Install with NPM

`bash
npm i jbrowse-nclist-cli -g
``