Paths configuration

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


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.


File for configuration.

Default is ${NEXTSTRAIN_HOME}/config.


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

Default is ${NEXTSTRAIN_HOME}/secrets.


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

Default is ${NEXTSTRAIN_HOME}/lock.


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/.


File for preserving command history across nextstrain shell invocations.

Default is ${NEXTSTRAIN_HOME}/shell-history.