Paths configuration

Nextstrain CLI uses various local filesystem paths for config and runtime data. If necessary, the defaults can be overridden by environment variables.

NEXTSTRAIN_HOME

Directory for config and other application data. Used as the basis for all other paths.

Default is ~/.nextstrain/, assuming a home directory is discernable. If not, .nextstrain (i.e. in the current directory) is used as a last resort.

NEXTSTRAIN_CONFIG

File for configuration.

Default is ${NEXTSTRAIN_HOME}/config.

NEXTSTRAIN_SECRETS

File for secrets (e.g. nextstrain.org tokens) managed by nextstrain login and nextstrain logout.

Default is ${NEXTSTRAIN_HOME}/secrets.

NEXTSTRAIN_LOCK

File for serializing access to other config files to prevent corruption and other bugs.

Default is ${NEXTSTRAIN_HOME}/lock.

NEXTSTRAIN_RUNTIMES

Directory for runtime-specific data, e.g. Singularity images or a Conda environment. Each runtime uses a subdirectory within here.

Default is ${NEXTSTRAIN_HOME}/runtimes/.

NEXTSTRAIN_SHELL_HISTORY

File for preserving command history across nextstrain shell invocations.

Default is ${NEXTSTRAIN_HOME}/shell-history.