pangyplot serve

Launch the PangyPlot web server in production mode (via gunicorn).

SYNOPSIS

pangyplot serve [OPTION]…

DESCRIPTION

Serves PangyPlot the same way pangyplot run does, but for production / remote use rather than local development. The two differ in three ways:

• serve binds 0.0.0.0 (reachable from outside the host or container); run binds 127.0.0.1 (localhost only).

• serve is backed by gunicorn, which is required — the command exits with an error if it is not installed; run uses Flask’s built-in development server.

• serve takes worker/thread/timeout tuning options.

Like run, it warms the datastore (building any missing paths, indexes, and skeletons) before the workers boot.

This command is what the Docker image’s default entrypoint invokes, so serving from the container is the same command you would type on a host: pangyplot serve --db <NAME> --ref <REF>.

OPTIONS

MANDATORY OPTIONS

--db NAME

Database name.

--ref STRING

Reference genome name.

DATABASE OPTIONS

--annotations NAME

Annotation set name (default: none).

--dir DIR

Database directory (default: datastore).

SERVER OPTIONS

--host ADDRESS

Address to bind to (default: 0.0.0.0, i.e. reachable from outside the host/container).

--port N

Port to serve app (default: 5700).

--workers N

Number of gunicorn worker processes (default: 1).

--threads N

Number of threads per gunicorn worker (default: 4).

--timeout N

gunicorn worker timeout in seconds (default: 120).