nextstrain-cli 1.1.3

Nextstrain command-line tool

nextstrain-cli

This is the Nextstrain command-line tool. It aims to provide access to Nextstrain components in a local environment with a minimum of fuss.

You can use it to run a pathogen build which makes use of components like sacra, fauna, and augur or view the results of such a build in our standard viewer, auspice.

Usage

This package provides a nextstrain program which provides access to a few commands. If you've installed this package (nextstrain-cli), you can just run nextstrain. Otherwise, you can run ./bin/nextstrain from a copy of the source code.

usage: nextstrain [-h] {build,view,update,check-setup,version} ...

Nextstrain command-line tool

optional arguments:
  -h, --help            show this help message and exit

commands:
  {build,view,update,check-setup,version}
    build               Run pathogen build
    view                View pathogen build
    update              Updates your local image copy
    check-setup         Tests your local setup
    version             Show version information

For more information on a specific command, you can run it with the --help option, for example, nextstrain build --help.

Installation

This tool is written in Python 3 and requires at least Python 3.5. Currently it is unpublished on PyPi while still in initial development, but you may still install the development version with pip (or pip3) like so:

pip install git+https://github.com/nextstrain/cli

or from a git clone or copy of the source code:

pip install .

If your system has both Python 2 and Python 3 installed side-by-side, you may need to use pip3 instead of pip (which often defaults to pip2).

We plan to publish a package on PyPi soon.

This tool also currently requires Docker. You can download and install the Docker Community Edition (CE) for your platform for free. After doing so, run nextstrain check-setup to ensure it works.