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To add the Oxford Nanopore apt repository, run the command below on a terminal window:
For Ubuntu 22:
sudo apt update sudo apt install wget wget -O- https://cdn.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add - echo "deb http://cdn.oxfordnanoportal.com/apt jammy-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list
For Ubuntu 20:
sudo apt update sudo apt install wget wget -O- https://cdn.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add - echo "deb http://cdn.oxfordnanoportal.com/apt focal-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list
For Ubuntu 18:
sudo apt update sudo apt install wget wget -O- https://cdn.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add - echo "deb http://cdn.oxfordnanoportal.com/apt bionic-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list
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Install MinKNOW using the command:
CPU version:
sudo apt update
sudo apt install ont-standalone-minknow-release
GPU version:
sudo apt update
sudo apt install ont-standalone-minknow-gpu-release
For GPU specifications, please refer to your sequencing device IT requirements document.
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Open the MinKNOW GUI from the applications list.
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Default installation directories
For the MinKNOW software:
/opt/ont/minknow
For the MinKNOW user interface:
/opt/ont/minknow-ui
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Location of the reads folder:
The reads folder is in
/var/lib/minknow/data
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Location of the log files:
The MinKNOW logs are located in
/var/log/minknow
The Dorado basecaller logs are located in/var/log/dorado
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Optional actionIf you have a proxy server and would like to set up MinKNOW using a proxy, follow the instructions below.
Open the
user_conf
file:/opt/ONT/MinKNOW/conf/user_conf
And edit the following portion of the file:
"proxy": {
"cereal_class_version": 0,
"use_system_settings": true,
"auto_detect": true,
"auto_config_script": "",
"https_proxy": "",
"proxy_bypass": ""
Edit the
https_proxy
setting, which should be in the style of:scheme://[username:password@]host:port or "http://domain\\username:password@host:port", where "scheme" is one of https, socks, socks4 or socks5.