nextstrain view
Visualizes a completed pathogen build in Auspice, the Nextstrain visualization app.
The data directory should contain sets of dataset files like:
<name>.json
or:
<name>_tree.json
<name>_meta.json
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 (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)
- --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: []