Python API client for MinKNOW

This package provides a Python client to access the MinKNOW APIs. You will need a compatible version of MinKNOW already installed to make use of this project.

To check for compatibility, look at the version of MinKNOW Core. The first two components of the MinKNOW Core version should match the first two components of the minknow_api version. For example, minknow_api 5.4.0 is compatible with any 5.4.x version of MinKNOW Core (which is part of the 22.12 release of MinKNOW).

See the main README in the git repository for more information about the MinKNOW API.

Using

The recommended way to get it is from PyPI using pip, but it can also be built from source (see BUILD.md in the top level of the git repository).

# Install minknow_api
> pip install minknow_api

# Verify API is installed correctly:
> python -m minknow_api.examples.list_sequencing_positions --host localhost

# Possible output if running MinKNOW locally:
#   Available sequencing positions on localhost:9502:
#   MN12345: running
#     secure: 8000

The package contains plenty of documentation in its docstrings, although for an overview of the MinKNOW APIs themselves you may prefer to read the API description files - see below for further discussion of these files. There are also examples in the minknow_api.examples submodule that show how to perform some common tasks.

Licence and Copyright

© 2023 Oxford Nanopore Technologies PLC.

API Specifications for MinKNOW is distributed under the Terms and Conditions of the Nanopore Community.

Troubleshooting

Bad metadata key

If you see the following error when connecting to the local machine:

grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
        status = StatusCode.UNAUTHENTICATED
        details = "Bad metadata key"

you can try setting the MINKNOW_API_USE_LOCAL_TOKEN environment variable to 1. Note that you will need to have MinKNOW's local guest mode enabled for this to work (it is enabled by default, but the setting can be changed via Mooneye).

Invalid local auth token

If you see the following error when connecting to a remote machine:

grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
        status = StatusCode.UNAUTHENTICATED
        details = "Invalid local auth token"

you can try setting the MINKNOW_API_USE_LOCAL_TOKEN environment variable to 0.

MissingMinknowSSlCertError

If you get a MissingMinknowSSlCertError exception, try setting the MINKNOW_TRUSTED_CA environment variable. This should be the path to the <data_dir>/rpc-certs/minknow/ca.crt file, where <data_dir> maps to C:\\data on Windows and /data on Ubuntu and MacOS platforms. You should use a copy of the file from the same version of MinKNOW as the one you are attempting to connect to.