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Install

metaWEPP offers multiple installation methods.

  1. Bioconda (Recommended)
  2. Dockerfile
  3. Shell Commands

Step 1: Create a new conda environment for metaWEPP. 

conda create --name metawepp-env
conda activate metawepp-env
conda config --env --add channels bioconda
conda config --env --add channels conda-forge
conda config --env --set channel_priority flexible
conda install metawepp

Note

⚠️ You can use conda install metawepp --solver=libmamba to enable a faster dependency resolution and installation.

Step 2: Confirm proper working by running the following command. This should print metaWEPP's help menu. 

run-metawepp help --cores 1

Step 3: Create a data directory and start analyzing your samples with metaWEPP. If you are running samples from multiple data directories, specify the .snakemake directory created in one run as the --conda-prefix for the others to avoid redundant creation of Snakemake conda environments.

Before trying the examples, please ensure that you have downloaded the simulated_metagenomic_sample into the data directory from here.

Note

⚠️ If you plan to generate a MAT for any species within the metaWEPP workflow using viral_usher, Docker access must be available on your system.

Option-2: Install via Dockerfile

Step 1: Clone the metaWEPP repository. 

git clone https://github.com/TurakhiaLab/metaWEPP.git
cd metaWEPP

Step 2: Build a Docker Image. 

cd docker
docker build -t metawepp .
cd ..

Step 3: Start and run Docker container. The command below will take you inside the Docker container with metaWEPP already installed. 

# -p <host_port>:<container_port> → Maps container port to a port on your host (Accessing Dashboard, NOT needed otherwise)
# Replace <host_port> with your desired local port (e.g., 100 or 8080)
docker run -it -p 80:80 metawepp

Step 4: Confirm proper working by running the following command. This should print metaWEPP's help menu. 

run-metawepp help --cores 1

All set to try the examples.

Note

⚠️ If you do not already have a MAT for a pathogen and wish to generate one using viral_usher, you must run viral_usher outside the metaWEPP Docker container and then copy the resulting MAT into the container. This is necessary because viral_usher invokes its own Docker instance during execution and will fail when run from within another Docker container.

Option-3: Install via Shell Commands (requires sudo access)

Step 1: Clone the repository. 

git clone https://github.com/TurakhiaLab/metaWEPP.git
cd metaWEPP
chmod +x run-metawepp

Step 2: Update ~/.bashrc for linux or ~/.zshrc for macOS. 

echo "
run-metawepp() {
    snakemake -s $PWD/Snakefile \"\$@\"
}
export -f run-metawepp
" >> ~/.bashrc

source ~/.bashrc

Step 3: Install Kraken. The following commands install kraken and also update the $PATH variable for running the tool easily. 

git clone https://github.com/DerrickWood/kraken2.git
cd kraken2
./install_kraken2.sh .
echo -e "\nexport PATH=\"$(pwd):\$PATH\"" >> ~/.bashrc
source ~/.bashrc
cd ..

Step 4: Install Minimap2, viral_usher, matplotlib, and snakemake. 

sudo apt-get install minimap2
pip install viral_usher matplotlib snakemake

Step 5: Install WEPP. 

git clone --recurse-submodules https://github.com/TurakhiaLab/WEPP.git
cd WEPP
chmod +x run-wepp

View the WEPP installation guide starting from Option 3 of the WEPP repository.

Step 6: Confirm proper working by running the following command. This should print metaWEPP's help menu. 

run-metawepp help --cores 1

All set to try the examples.

Note

⚠️ If you plan to generate a MAT for any species within the metaWEPP workflow using viral_usher, Docker access must be available on your system.