nanoporetech / nanoporetech/minknow_api

rebasecalling after a run using the api

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Dominant language
Python
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Description

Hey,

Is it possible to start basecalling after a run has finished ? I tried to (using chatgpt/copilot) but it doesn't seem to find a solution.

As I understand these should be the steps :

  1. connect to MinKNOWN manager
  2. get the basecaller endpoint
  3. connect to basecaller service and start a basecall run ?
import grpc
from minknow_api.manager import Manager
from minknow_api.basecaller_service import Basecaller

manager = Manager(host="localhost", port=9501)

# 2. Discover available basecaller API ports
api_endpoints = manager.basecaller() 
# in my case returned server:localhost port:9504 

# 3. Connect to the basecaller service
channel = grpc.insecure_channel(f"{basecaller_host}:{basecaller_port}")
basecaller = Basecaller(channel)

# 4. Start basecalling
response = basecaller.start_basecalling(
    input_reads_directories=["/path/pod5_skip"],
    output_reads_directory="/path/basecalls",
    configuration="dna_r10.4.1_e8.2_400bps_sup@v5.0.0"
)

This however doesn't seem the way as its giving me : status = StatusCode.UNAVAILABLE

Did I miss something ? Is there an example somewhere ? I checked start_protocol.py but that needs to connect to a position, which I don't have cause its a server not connected to ONT device directly. (its after the run)

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with start_protocol.py and the Manager and Basecaller usage shown in the issue, then trace how the basecaller endpoint is exposed for completed runs. Reproduce the StatusCode.UNAVAILABLE response with the provided connection flow. Done means documenting or demonstrating a working post-run basecalling workflow for a server without a directly connected ONT device.

Written by the indexing model from the issue text.

Assessment

Tech stack
grpc, python
Domain
api, documentation
Issue type
Documentation
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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