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: []

Named Arguments

--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: []