The final setup I went with can be found below. It was expensive (around 4000 for the laptop in early 2022), but should be able to achieve live basecalling for two MinION devices at the same time. Overall specs of my laptop:

Minimum IT requirements for MinION from ONT: minion-it-reqs.pdf

The remainder of this protocol assumes you have completed all of the preliminary setup steps that are common with any new CPU.

Install CUDA toolkit - http://developer.nvidia.com/cuda-toolkit :

wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-ubuntu2204.pin
sudo mv cuda-ubuntu2204.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget http://developer.download.nvidia.com/compute/cuda/11.7.0/local_installers/cuda-repo-ubuntu2204-11-7-local_11.7.0-515.43.04-1_amd64.deb
sudo dpkg -i cuda-repo-ubuntu2204-11-7-local_11.7.0-515.43.04-1_amd64.deb
sudo cp /var/cuda-repo-ubuntu2204-11-7-local/cuda-*-keyring.gpg /usr/share/keyrings/
sudo apt-get update
sudo apt-get -y install cuda

Install Boost

sudo apt install libboost-all-dev

The process at this link was instrumental to this protocol. It is recreated and simplified here. ORIGINAL PROTOCOL. It was written for Pop!_OS 21.04. The following protocols also work with Pop!_OS 22.04. I would follow the steps at the link rather than here so you get a broader context of the actions you are performing on your system.

#Add ONT Focal Repository (Pop!_OS 22.04)
# update packages list
sudo apt-get update
# check for and install wget if needed
if [ $(dpkg-query -W -f='${Status}' wget 2>/dev/null | grep -c "ok installed") -eq 0 ];
then
  sudo apt --yes install wget;
fi
# add the key
wget -O- http://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add -
# add the focal repo
echo "deb http://mirror.oxfordnanoportal.com/apt focal-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list

#sudo apt update (Pop!_OS 22.04)
sudo apt update

#Check for access to ONT files (Pop!_OS 22.04)
apt policy minknow-core-minion-nc

Add the Focal repos:

#Create a new file and edit in nano 
sudo nano /etc/apt/sources.list.d/system-focal.sources
```Copy and paste the following into your file:





```X-Repolib-Name: Pop_OS System Sources<br/>Enabled: yes<br/>Types: deb deb-src<br/>URIs: http://us.archive.ubuntu.com/ubuntu/<br/>Suites: focal focal-security focal-updates focal-backports<br/>Components: main restricted universe multiverse<br/>X-Repolib-Default-Mirror: http://us.archive.ubuntu.com/ubuntu/

cat system-focal.sources

Pin the Focal repos. Start by creating another new file with nano:

sudo nano /etc/apt/preferences.d/focal-default-settings

Copy and paste the following into your file:

Check that is was created correctly

cat focal-default-settings

sudo apt update

Install MinKNOW and required packages

sudo apt install \
  minknow-core-minion-nc \
  ont-kingfisher-ui-minion \
  ont-bream4-minion \
  ont-configuration-customer-minion \
  ont-jwt-auth \
  ont-vbz-hdf-plugin

Install ONT Guppy

sudo apt install ont-guppy

which guppy_basecaller

guppy_basecaller --version

Setup the MinKnow service

sudo /opt/ont/minknow/bin/config_editor --conf application \
  --filename /opt/ont/minknow/conf/app_conf \
  --set guppy.server_executable="/opt/ont/guppy/bin/guppy_basecall_server" \
  --set guppy.client_executable="/opt/ont/guppy/bin/guppy_basecall_client" \
  --set guppy.gpu_calling=1 \
  --set guppy.num_threads=16 \
  --set guppy.ipc_threads=2

systemctl restart minknow.service

systemctl status minknow.service

sudo nano /lib/systemd/system/guppyd.service
```Copy the following to your new file:





```[Unit]<br/>Description=Service to manage the guppy basecall server.<br/>Documentation=http://community.nanoporetech.com/protocols/Guppy-protocol/v/GPB_2003_v1_revQ_14Dec2018<br/><br/>[Service]<br/>Type=simple<br/>ExecStart=/opt/ont/guppy/bin/guppy_basecall_server --log_path /var/log/guppy --config dna_r9.4.1_450bps_fast.cfg --port 5555 -x cuda:all <br/>Restart=always<br/>User=root<br/>MemoryLimit=8G<br/>MemoryHigh=8G<br/>CPUQuota=200%<br/><br/>[Install]<br/>Alias=guppyd.service<br/>WantedBy=multi-user.target

Check the file:

cat /lib/systemd/system/guppyd.service

systemctl enable guppyd.service

systemctl restart guppyd.service

MinKNOW GUI should now be available in your programs. Validate that it opens correctly.

Changes to MinKnow file permissions at the bottom here:

http://gringer.gitlab.io/presentation-notes/2021/10/08/gpu-calling-in-minknow/

"For my computer, there’s an issue with MinKNOW not being able to access or create files. As a “nuclear” option, Miles Benton suggested changing the user and group for the minknow service to root"

sudo service minknow stop
sudo perl -i -pe 's/(User|Group)=minknow/$1=root/' /lib/systemd/system/minknow.service
sudo systemctl daemon-reload
sudo service minknow start

Per this document: http://denbi-nanopore-training-course.readthedocs.io/en/latest/read_qc/MinionQC.html

Install R: http://cran.r-project.org/

Install MinionQC: http://github.com/roblanf/minion_qc

Install R:

# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
wget -qO- http://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb http://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

sudo apt install --no-install-recommends r-base

install.packages(c("data.table", 
                   "futile.logger",
                   "ggplot2",
                   "optparse",
                   "plyr",
                   "readr",
                   "reshape2",
                   "scales",
                   "viridis",
                   "yaml"))

Install Bioconductor:

In an R command window:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.15")

Install Anaconda:

from: http://www.digitalocean.com/community/tutorials/how-to-install-the-anaconda-python-distribution-on-ubuntu-22-04

cd /tmp

curl http://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-x86_64.sh --output anaconda.sh

sha256sum anaconda.sh

bash anaconda.sh

source ~/.bashrc

conda list

conda search "^python$"

conda create --name my_env python=3

conda activate my_env

python --version

conda install --name my_env35 numpy

Install NGSpeciesID: http://github.com/ksahlin/NGSpeciesID

conda create -n NGSpeciesID python=3.6 pip 
conda activate NGSpeciesID

conda install --yes -c conda-forge -c bioconda medaka==0.11.5 openblas==0.3.3 spoa racon minimap2
pip install NGSpeciesID

conda activate NGSpeciesID

mkdir test_ngspeciesID
cd test_ngspeciesID

curl -LO http://raw.githubusercontent.com/ksahlin/NGSpeciesID/master/test/sample_h1.fastq

NGSpeciesID --ont --fastq sample_h1.fastq --outfolder ./sample_h1 --consensus --medaka

You should now be ready to begin sequencing runs.

Since this protocol was first written, MinKnow needed an update for the 10.4.1 Flongle cells. The steps to perform the update can be found below:

sudo apt install minknow-core-minion-nc=5.3.1-focal
sudo apt install ont-bream4-minion=7.3.5-1~focal
sudo apt install ont-configuration-customer-minion=5.3.8-1~focal
sudo apt install ont-kingfisher-ui-minion=5.3.6-1~focal

sudo apt-get update 
sudo apt-get install minion-nc

sudo chmod -R a+rw /var/lib/minknow/

sudo service minknow stop
sudo perl -i -pe 's/(User|Group)=minknow/$1=root/' /lib/systemd/system/minknow.service
sudo systemctl daemon-reload
sudo service minknow start


sudo apt install cuda
conda install -c bioconda seqkit

python -m venv venv --prompt duplex
. venv/bin/activate
pip install duplex_tools