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
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.
- --conda
Run commands with access to a fully-managed Conda environment.
- --singularity
Run commands inside a container image using Singularity.
development options
These should generally be unnecessary unless you’re developing Nextstrain.
- --image
Container image name to use for the Nextstrain runtime (default: “nextstrain/base” for Docker and AWS Batch, docker://nextstrain/base for Singularity)
Default: “nextstrain/base”
- --exec
Program to run inside the runtime
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: []