Command-line interface¶

Pipelines are executed with the biocomp command (installed by pip install biocomposer).

biocomp run [--modal] run/run_pipeline.py --env .env

Flags¶

Flag	Scope	Meaning
`--env <path>`	both	env file with API keys (default `.env`)
`--clean`	both	clear previous outputs first
`--modal`	both	run on Modal instead of locally
`--gpu T4`	modal	GPU type (default `A10G`)
`--memory 32768`	modal	sandbox memory in MB (default `8192`)
`--shell`	modal	drop into an interactive sandbox shell

Local runs require Docker and bv; Modal runs require modal setup. See Installation.