nextstrain shell

Start a new shell inside a Nextstrain runtime to run ad-hoc commands and perform debugging.

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

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)

--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

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.

Default: []

--envdir

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.

Default: []

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: “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: []