jheffer/pyminknow repository overview

⁠minKNOW mock server

This code will emulate a Oxford Nanopore Technologies⁠ gene sequencing device (e.g. minION⁠ or minKNOW) using its gRPC Remote Procedure Calls LIMS interface⁠ to interact with its embedded software. This package is designed to form part of a software development environment to facilitate rapid prototyping and automated testing.

⁠Glossary

• minKNOW device manager (host software)
• gridION a physical device containing an array of sequencing devices
• minION a physical sequencing device

⁠See also

• Developed at The University of Sheffield, IT Services, Research & Innovation⁠.
• pyminknow⁠ at PyPi
• pyminknow⁠ at Docker Hub
• pyminknow⁠ at GitHub
• pyminknow⁠ at FigShare

⁠Installation

$ pip install pyminknow

⁠Usage

The service may run in a container or in a Python environment. To see the usage reference, run:

$ python pyminknow --help

⁠Test client

You may use client.py to test the functionality of the server. To get help, run:

$ python client.py --help

Unit tests may be used to systematically test the server functionality.

$ python -m unittest

⁠Container

The container is based on Debian Linux and uses Python 3.7 as defined in the Dockerfile. You may build and run the container using the commands below.

$ docker build --tag pyminknow:latest .
$ docker run --name minit --publish 5901:5901 -publish 22:22 -d pyminknow:latest
# Start the SSH service
$ docker exec -it --user root minit service ssh start

⁠Python

You should do this inside a Python 3.7 virtual environment. Install packages and then run the service.

$ pip install pyminkow
$ python -m pyminknow