5.3 BioLine Host-Side Scripts

Host-side scripts coordinate BioLine with the local isolated task under the current execution lane. They do not select a static pipeline or Skill subset.

• gateway.sh accepts the objective and inputs, starts planning, and presents the Flow, input bindings, and downstream target for confirmation.
• orchestrator.sh records the Flow/Job lifecycle: discover and inspect a Flow, submit only after confirmation, then download and finalize successful results into stage.
• prepare_downstream.sh resolves an exact BioLine Tool NAME:VERSION, exports its summary/config, checks the downstream marker and empty fixed-command fields, and pulls that version on demand.
• run_downstream.sh runs the script generated and saved for the current task. Stage and task reproducibility material are read-only mounts, networking is disabled, and the analysis output directory is writable.
• attach.sh is not used to append analysis capabilities to a running container or modify a published Tool. A new analysis request should recheck suitable Tools and inputs, then create a task-specific script.
• stop_downstream.sh follows the task pull ledger for restricted cleanup. It may attempt non-forced removal only when this task pulled an image that was absent beforehand, its identity has not changed, and it is not shared or in use. It does not remove pre-existing images or run prune.

Every analysis capability is a BioLine Tool. The five historical images are migration inventory only; if no existing Tool or Flow fits, use the separate authoring and confirmation workflow.