Pipelines are executed with the biocomp command (installed by
pip install biocomposer).
biocomp run [--modal] run/run_pipeline.py --env .env
| 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
:doc:`installation`.
modal volume get biocomp results/<tool>_output_1/stdout/<file> ./<file>