nextstrain view

Visualizes a completed pathogen builds or narratives in Auspice, the Nextstrain visualization app.

<path> may be a dataset (.json) file or narrative (.md) file to start Auspice and directly open the specified dataset or narrative in a browser. Adjacent datasets and/or narratives may also be viewable as an appropriate data directory for Auspice is automatically inferred from the file path.

<path> may also be a directory with one of the following layouts:

<path>/
├── auspice/
│   └── *.json
└── narratives/
    └── *.md

<path>/
├── auspice/
│   └── *.json
└── *.md

<path>/
├── *.json
└── narratives/
    └── *.md

<path>/
├── *.json
└── *.md

Dataset and narrative files will be served, respectively, from auspice and/or narratives subdirectories under the given <path> if the subdirectories exist. Otherwise, files will be served from the given directory <path> itself.

If your pathogen build directory follows our conventional layout by containing an auspice directory (and optionally a narratives directory), then you can give nextstrain view the same path as you do nextstrain build.

Note that by convention files named README.md or group-overview.md will be ignored for the purposes of finding available narratives.

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

Positional Arguments

<path>

Path to a directory containing dataset JSON and/or narrative Markdown files for Auspice, or a directory containing an auspice/ and/or narratives/ directory, or a specific dataset JSON or narrative Markdown file.

Named Arguments

--help, -h

Show a brief help message of common options and exit

--open

Open a web browser automatically

Default: False

--no-open

Do not open a web browser automatically (the default)

Default: True

--allow-remote-access

Allow other computers on the network to access the website (alias for –host=0.0.0.0)

--host

Listen on the given hostname or IP address instead of the default “127.0.0.1”

Default: “127.0.0.1”

--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)

--ambient

Run commands in the ambient environment, outside of any container image.

--conda

Run commands with access to a fully-managed Conda environment.

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: []