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 </config/file>.
Default is {${NEXTSTRAIN_HOME}}/config.
NEXTSTRAIN_SECRETS
File for secrets (e.g. nextstrain.org tokens) managed by /commands/login and /commands/logout.
Default is {${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 /commands/shell invocations.
Default is {${NEXTSTRAIN_HOME}}/shell-history.