view.rst

nextstrain view

nextstrain view

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

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.

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.

options

--help, -h

Show a brief help message of common options and exit

--help-all

Show a full help message of all options and exit

--open

Open a web browser automatically (the default)

--no-open

Do not open a web browser automatically

--allow-remote-access

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

--host <ip/hostname>

Listen on the given hostname or IP address instead of the default 127.0.0.1. You may also set the HOST environment variable to change the default.

--port <number>

Listen on the given port instead of the default port 4000. You may also set the PORT environment variable to change the default.

runtime selection options

Select the Nextstrain runtime to use, 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 or managed environment.

--conda

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

--singularity

Run commands inside a container image using Singularity.

runtime options

Options shared by all runtimes.

--env <name>[=<value>]

Set the environment variable <name> to the value in the current environment (i.e. pass it thru) or to the given <value>. May be specified more than once. Overrides any variables of the same name set via --envdir. When this option or --envdir is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are AUGUR_RECURSION_LIMIT, AUGUR_MINIFY_JSON, AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_SESSION_TOKEN, ID3C_URL, ID3C_USERNAME, ID3C_PASSWORD, RETHINK_HOST, and RETHINK_AUTH_KEY. Pass those variables explicitly via --env or --envdir if you need them in combination with other variables.

--envdir <path>

Set environment variables from the envdir at <path>. May be specified more than once. An envdir is a directory containing files describing environment variables. Each filename is used as the variable name. The first line of the contents of each file is used as the variable value. When this option or --env is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. See the description of --env for more details.

development options

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

--image <image>

Container image name to use for the Nextstrain runtime (default: nextstrain/base for Docker and AWS Batch, docker://nextstrain/base for Singularity)

--exec <prog>

Program to run inside the runtime

development options for --docker

--augur <dir>

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

--auspice <dir>

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

--fauna <dir>

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

--sacra <dir>

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

--docker-arg ...

Additional arguments to pass to docker run

In some contexts, it may be preferable to provide environment variables instead of command-line options:

HOST

Hostname or IP address on which to listen by default. Ignored if --host or --allow-remote-access is provided.

PORT

Port on which to listen by default. Ignored if --port is provided.