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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Call standalone Dorado from minKNOW installation #778

Closed mgperry closed 4 months ago

mgperry commented 5 months ago

Issue Report

Please describe the issue:

Hi, I was wondering if it is possible to access the standalone dorado executable using just the minKNOW installation? ie without having to install dorado twice on the same machine. I can't find the binary anywhere in the /opt/ont/ folder.

Apologies if this is the wrong place, I can't find a separate repository for dorado_basecall_server.

Steps to reproduce the issue:

Fresh install of minKNOW using instructions online for apt.

Run environment:

minKNOW: Package: minknow-core-minion-nc Version: 5.9.7

Running on Ubuntu 22.04

malton-ont commented 5 months ago

Hi @mgperry,

The standalone dorado executable is not included in the minknow 5.9 installation. MinKNOW performs all basecalling via the dorado_basecall_server. It is safe to install the standalone package separately, but you will need to run it directly from the command line