Documentation

Installation

pip install .

Usage

Main script available as crispr-screen-viewer with subcommands.

Manage database

See crispr-screen-viewer database -h

Construct database from input files. Example dataset is in the data directory.

Run the viewer

via script

See crispr-screen-viewer launch -h. Requires a database constructed by the above command.

Gunicorn

Create a python module to create the server object, called (for example) test_crsv.py

from crispr_screen_viewer import launch
from crispr_screen_viewer.functions_etc import get_resource_path

# Use the provided example data
db_path = get_resource_path('tests/test_data')
server = launch.get_server(data_path=db_path)

Then call (with your desired port):

gunicorn --bind 0.0.0.0:8050 test_crsv:server

Gunicorn via docker

Put your data in the src/crispr_screen_viewer/data directory before building the image, then run

docker run \
	--user appuser \
	-p 8050:8050 \
	--workdir /app/src/crispr_screen_viewer/ \
	<docker image> \
	gunicorn --bind 0.0.0.0:8050 launch:"get_server()"