Setting up environment for ONT QC

Use WSL to run unix (for windows, you don’t need this for mac or linux OS’s)

wsl --install
wsl.exe -d Ubuntu
# set username and password

Step 1: Install conda

# make directory
cd ~
mkdir ~/miniconda3/

# download installer
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
## OR PUT miniconda.sh INTO FOLDER FROM HARD DRIVE

## to open a location from WSL terminal in file explorer run
explorer.exe .

# run installer
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

# remove installer 
rm ~/miniconda3/miniconda.sh
# refresh shell
source ~/miniconda3/bin/activate
# initialise conda
conda init --all

Step 2: Log in to unix environment after closing PowerShell (you don’t need this for Mac or linux OS’s)

# Unix user account: 
# password: 

Step 3: Create directory to store repository locally

mkdir ~/Tools/

# clone repository to newly created directory
git clone https://github.com/centre-pathogen-genomics/CPGIH_Utility.git ~/Tools/CPGIH_Utility
## OR PUT /CPGIH_Utility/ INTO FOLDER FROM HARD DRIVE

Step 4: Create conda environment into which you will install the software

conda create -n cpgih_utility -y

# activate the conda environment
conda activate cpgih_utility

# install the required software 
conda install -c bioconda -c conda-forge kraken2 shovill seqkit csvtk flye emu python=3.12.3 -y
conda install anaconda::gawk

Step 5: Update $BRIDGE_SCRIPT_DIR and $BRIDGE_WORKING_DIR. These two variables need to be set to the local directory of the CPGIH_Utility repo scripts directory and the working directory of the machine respectively.

eg. BRIDGE_SCRIPT_DIR=/home/cpgih/Tools/CPGIH_Utility/Scripts and BRIDGE_WORKING_DIR=/mnt/c/Users/charl/OneDrive/Desktop.

# Set these with the following:

conda env config vars set BRIDGE_SCRIPT_DIR=/home/cpgih/Tools/CPGIH_Utility/Scripts
conda env config vars set BRIDGE_WORKING_DIR=/mnt/c/Users/charl/OneDrive/Desktop

# restart env to load
conda deactivate
conda activate cpgih_utility
# confirm location is set
conda env config vars list

Step 6: Setup DBs

i. kraken2 database

# make kraken directory
mkdir ~/kraken2_db

# download db
curl -o ~/kraken2_db/kraken2_db.tar.gz https://genome-idx.s3.amazonaws.com/kraken/k2_standard_16gb_20241228.tar.gz
## OR PUT kraken2_db.tar.gz INTO FOLDER FROM HARD DRIVE

# extract db
tar -xzf ~/kraken2_db/kraken2_db.tar.gz -C ~/kraken2_db 

# check it worked AND THE COMPUTER CAN RUN IT
kraken2-inspect --db ~/kraken2_db | head

# delete tarball to save space
rm ~/kraken2_db/kraken2_db.tar.gz 

# tell conda where to find it
conda env config vars set KRAKEN2_DEFAULT_DB=$HOME/kraken2_db

# restart env to load
conda deactivate
conda activate cpgih_utility
# confirm location is set
conda env config vars list

ii. emu database

# make emu directory
mkdir ~/emu_db

# tell conda where to find it
export EMU_DATABASE_DIR=$HOME/emu_db/
# enter db directory
cd ${EMU_DATABASE_DIR}

# download db
pip install osfclient
osf -p 56uf7 fetch osfstorage/emu-prebuilt/emu.tar
## OR PUT emu.tar INTO FOLDER FROM HARD DRIVE

# extract
tar -xvf emu.tar

# remove tarball
rm emu.tar

Step 7: Reload tools after update

# login to wsl and change location
wsl
cd /home/cpgih

# delete Tools/
sudo rm -r Tools

# create directory to store repository locally
mkdir ~/Tools/

# clone repository to newly created directory
git clone https://github.com/centre-pathogen-genomics/CPGIH_Utility.git ~/Tools/CPGIH_Utility

Step 8: Wrapper scripts setup

# Wraps both illumina_genomesqc.sh, ont_genomesqc.sh as command line application
# Add scripts directory to the path of the machine:

echo 'export PATH=$PATH:[REPO_PATH]/Scripts' | tee -a ~/.bashrc >> ~/.zshrc

eg. `echo 'export PATH=$PATH:/home/cpgih/Tools/CPGIH_Utility/Scripts' | tee -a ~/.bashrc >> ~/.zshrc

Step 9: How to change the file location with the wrapper script?

You can change the path to your input files by running this code again and changing the location

conda env config vars set BRIDGE_WORKING_DIR=/mnt/c/Users/charl/OneDrive/Desktop