nextstrain shellď
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 Argumentsď
- <directory>
Path to pathogen build directory
- ...
Additional arguments to pass to the executed program
Default: []
Named Argumentsď
- --help, -h
Show a brief help message of common options and exit
runtime selection optionsď
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 optionsď
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 âenvdir. When this option or âenvdir is given, the default behaviour of automatically passing thru several âwell-knownâ variables is disabled. The âwell-knownâ 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 âenv or âenvdir 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 âenv is given, the default behaviour of automatically passing thru several âwell-knownâ variables is disabled. See the description of âenv for more details.
Default: []
development optionsď
These should generally be unnecessary unless youâre developing Nextstrain.
- --image
Container image name to use for the Nextstrain runtime (default: ânextstrain/baseâ for Docker and AWS Batch, docker://nextstrain/base for Singularity)
Default: ânextstrain/baseâ
- --exec
Program to run inside the runtime
Default: âbashâ
development options for âdockerď
- --augur
Replace the imageâs copy of augur with a local copy
- --auspice
Replace the imageâs copy of auspice with a local copy
- --fauna
Replace the imageâs copy of fauna with a local copy
- --sacra
Replace the imageâs copy of sacra with a local copy
- --docker-arg
Additional arguments to pass to docker run
Default: []