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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 python=3.11
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

⚠️ Python 3.11 is required. The latest wepp builds that metaWEPP depends on are only available for Python 3.11, so environments pinned to Python 3.12 silently fall back to an older wepp, and Python 3.13 fails to solve altogether.

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.