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Command-line reference

ROBIN exposes a robin CLI (Click). This section documents each command group. For a first run, see Installation and Quickstart.

Command tree

Command Purpose
robin workflow Watch a directory of BAMs and run the selected analysis pipeline (Ray, NiceGUI optional).
robin list-job-types Print job types and queue layout.
robin list-panels / add-panel / remove-panel Manage target gene panels.
robin utils … Models, ClinVar, reference/panel staging, MGMT summaries.
robin password … Set the NiceGUI login password.

Run robin --help and robin <command> --help for the exact options shipped with your install.

Disclaimer prompt

Many commands that change state or start processing show a disclaimer and require you to type I agree exactly (research-use acknowledgment).

Environment variables (selected)

Variable Effect
GITHUB_TOKEN Used by robin utils update-models when assets are fetched from private GitHub.
ROBIN_PROCESS_LARGE_BAMS If enabled, warns that large-BAM mode must not be used alongside live runs.
LJ_BAM_THREADS Optional tuning for multi-threaded BAM handling (see README — Performance).

First-time startup experience

When you run robin workflow, ROBIN performs model checks, optional reference validation, the research disclaimer (I agree), and (if the GUI is enabled) GUI password prompts. See What happens at startup.

Web interface

For a browser user guide (navigation, each screen, reading results), see Using ROBIN.

See also