Clade assignment, mutation calling, and sequence quality checks. This is the command line version of nextclade.

• Version: 0.12.0
• Added: February, 2021
• Link: https://github.com/nextstrain/nextclade/tree/master/packages/nextclade_cli

See versions of nextclade which are available:

$ module avail nextclade

Load one version into your environment and run it:

$ module load nextclade/0.12.0
$ nextclade.js

Notes from the sysadmin during installation:

$ sudo yum install rh-nodejs12-nodejs.x86_64
$ cd /tmp
$ git clone https://github.com/nextstrain/nextclade.git
$ cd nextclade
$ git checkout 0.12.0
$ cd packages/web
$ cp .env.example .env
$ export PATH=$PATH:/opt/rh/rh-nodejs12/root/usr/bin
$ npm config set cache /tmp/aorth-npm
$ npm install yarn
$ npx yarn cli:prod:build
$ sudo mkdir -p /export/apps/nextclade/0.12.0/bin
$ sudo cp -r ../cli/dist/* /export/apps/nextclade/0.12.0/bin

Note: nextclade's command line utility is written in JavaScript so we need Node.js to install it. This requires a bit of extra work to make sure that npm doesn't write thousands of packages to its cache on our network-based home directory.