snakemake-logger-plugin-panoptes 0.1.1

Snakemake logger plugin that forwards workflow events to a panoptes server.

snakemake-logger-plugin-panoptes

A Snakemake 9 logger plugin that forwards workflow events to a running panoptes server, replacing the legacy --wms-monitor integration that was removed in Snakemake 9.

Install

pip install snakemake-logger-plugin-panoptes

Use

Start a panoptes server (see the panoptes README), then run Snakemake with the plugin enabled:

snakemake \
    --cores 1 \
    --logger panoptes \
    --logger-panoptes-address http://127.0.0.1:5000

You can also point at the address via an environment variable:

export SNAKEMAKE_LOGGER_PANOPTES_ADDRESS=http://127.0.0.1:5000
snakemake --cores 1 --logger panoptes

Settings

Flag	Env var	Default	Description
--logger-panoptes-address	SNAKEMAKE_LOGGER_PANOPTES_ADDRESS	(required)	Base URL of the panoptes server.
--logger-panoptes-timeout	—	10.0	Per-request HTTP timeout in seconds.

How it works

On workflow start the plugin calls GET /create_workflow to register a new workflow with the panoptes server and remembers the returned workflow id. It then translates Snakemake LogEvent records (JOB_INFO, JOB_STARTED, JOB_FINISHED, JOB_ERROR, SHELLCMD, PROGRESS, ERROR, RUN_INFO) into the JSON message format that panoptes' /update_workflow_status endpoint already understands.

Network errors are logged but never crash the workflow.

Development

pip install -e .[dev]   # editable install with test deps
pytest

License

MIT