nextstrain view

Visualizes a completed pathogen build in Auspice, the Nextstrain visualization app.

The data directory should contain sets of Auspice JSON¹ files like

<name>.json

or

<name>_tree.json <name>_meta.json

The viewer runs inside a container, which requires Docker. Run nextstrain check-setup to check if Docker is installed and works.

¹ <https://nextstrain.github.io/auspice/introduction/how-to-run#input-file-formats>

usage: nextstrain view [options] <directory>
       nextstrain view --help

Positional Arguments

<directory>

Path to directory containing JSONs for Auspice

Named Arguments

--help, -h

Show a brief help message of common options and exit

--allow-remote-access

Allow other computers on the network to access the website

Default: False

--port

Listen on the given port instead of the default port 4000

Default: 4000

runner selection options

Select the method for running a Nextstrain computing environment, if the default is not suitable.

--docker

Run commands inside a container image using Docker. (default)

--native

Run commands on the native host, outside of any container image.

development options

These should generally be unnecessary unless you’re developing Nextstrain.

--image

Container image name to use for the Nextstrain computing environment

Default: “nextstrain/base”

--exec

Program to run inside the build environment

Default: “auspice”

development options for –docker

--augur

Replace the image’s copy of augur with a local copy

--auspice

Replace the image’s copy of auspice with a local copy

--fauna

Replace the image’s copy of fauna with a local copy

--sacra

Replace the image’s copy of sacra with a local copy

--docker-arg

Additional arguments to pass to docker run

Default: []