Environment variables
The Seqera CLI reads the following environment variables for authentication, for pointing development builds at a backend, and for controlling CLI behavior.
Connection and authentication
| Variable | Description |
|---|---|
SEQERA_ACCESS_TOKEN | Platform access token for non-interactive use. When set, the CLI skips the browser login flow and uses this token directly. |
TOWER_ACCESS_TOKEN | Platform personal access token used instead of browser login. |
SEQERA_AI_BACKEND_URL | Co-Scientist backend endpoint used by the CLI. |
SEQERA_AUTH_DOMAIN | Platform API base URL used for browser-based login. |
SEQERA_AUTH_CLI_CLIENT_ID | OAuth client ID for the Seqera CLI. Defaults to seqera_ai_cli. |
SEQERA_PLATFORM_API_URL | Platform API endpoint used by seqera info. |
SEQERA_AUTH_REDIRECT_PORT | Local port for the browser login callback. Defaults to 53682. |
SEQERA_AUTH_CALLBACK_TIMEOUT_MS | How long the CLI waits for the browser login callback, in milliseconds. |
SEQERA_BROWSER_AUTO_OPEN | Set to false to print the login URL instead of opening a browser, for example on a remote host. |
note
You need SEQERA_AI_BACKEND_URL, SEQERA_AUTH_DOMAIN, and SEQERA_AUTH_CLI_CLIENT_ID only when you point a development build at the hosted Co-Scientist backend. See Authentication for the full setup.
CLI behavior
| Variable | Description |
|---|---|
SEQERA_AI_CWD | Working directory for local operations. Defaults to the directory you start the CLI in. |
SEQERA_CLI_OUTPUT_FORMAT | Set to json to make JSON the default output format for seqera info. |
SEQERA_THEME | Force the light or dark terminal theme instead of detecting it. |
SEQERA_REDUCE_MOTION | Disable tip rotation animations. |
SEQERA_LOG_LEVEL | CLI log level. |
SEQERA_LOG_FILE | Path of the CLI diagnostic log file. Defaults to /tmp/seqera-cli-diag.jsonl. |
SEQERA_DISABLE_LSP_DOWNLOAD | Set to true to stop the CLI from downloading the Nextflow language server. See Nextflow LSP. |
Learn more
- Authentication: Log in, log out, and manage tokens
- Installation: Install, update, and configure the CLI
- CLI: Seqera CLI commands and options
- Skills: Built-in skills, slash commands, and session limits