nextstrain shell
Start a new shell inside the Nextstrain containerized build environment to run ad-hoc commands and perform debugging.
The shell runs inside a container, which requires Docker. Run nextstrain check-setup to check if Docker is installed and works.
usage: nextstrain shell [options] <directory> [...]
nextstrain shell --help
Positional Arguments
- <directory>
Path to pathogen build directory
- ...
Additional arguments to pass to the executed program
Default: []
options
- --help, -h
Show a brief help message of common options and exit
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)
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: “bash”
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: []