Install

WEPP offers multiple installation methods.

1. Bioconda (Recommended)
2. Docker image from DockerHub
3. Dockerfile
4. Shell Commands

Option-1: Install via Bioconda (Recommended)

Step 1: Create a new conda environment for WEPP.

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

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

run-wepp help --cores 1 --use-conda

Step 3: Create a data directory and start analyzing your samples with WEPP. 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.

All set to try the examples.

Option-2: Install via DockerHub

The Docker image includes all dependencies required to run WEPP.

Step 1: Get the image from DockerHub

docker pull pranavgangwar/wepp:latest

Step 2: Start and run Docker container. The command below will take you inside the docker container with WEPP 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., 80 or 8080)
# Use this command if your datasets can be downloaded from the Web
docker run -it -p 80:80 pranavgangwar/wepp:latest

# Use this command if your datasets are present in your current directory
docker run -it -p 80:80 -v "$PWD":/WEPP -w /WEPP pranavgangwar/wepp:latest

Step 3: Confirm proper working by running the following command. This should print WEPP's help menu.

run-wepp help --cores 1 --use-conda

All set to try the examples.

Note

⚠️The Docker image is currently built for the linux/amd64 platform. While it can run on arm64 systems (e.g., Apple Silicon or Linux aarch64) via emulation, this may lead to reduced performance.

Option-3: Install via Dockerfile

The Dockerfile contains all dependencies required to run WEPP.

Step 1: Clone the repository

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

Step 2: Build a Docker Image

cd docker
docker build -t wepp . 
cd ..

Step 3: Start and run Docker container. The command below will take you inside the docker container with the view of the current directory.

# -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., 80 or 8080)
docker run -it -p 80:80 -v "$PWD":/workspace -w /workspace wepp

All set to try the examples.

Option-4: Install via Shell Commands (requires sudo access)

Users without sudo access are advised to install WEPP via Docker Image.

Step 1: Clone the repository

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

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

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

source ~/.bashrc

Step 3: Install dependencies (might require sudo access) WEPP depends on the following common system libraries, which are typically pre-installed on most development environments:

- wget
- curl
- pip
- build-essential 
- python3-pandas
- pkg-config
- zip
- cmake 
- libtbb-dev
- libprotobuf-dev
- protobuf-compiler
- libopenmpi-dev
- snakemake
- conda
- nodejs(v18+)
- nginx

For Ubuntu users with sudo access, if any of the required libraries are missing, you can install them with:

sudo apt-get update
sudo apt-get install -y wget pip curl python3-pip build-essential python3-pandas pkg-config zip cmake libtbb-dev libprotobuf-dev protobuf-compiler snakemake nginx

Note: WEPP expects the python command to be available. If your system only provides python3, you can optionally set up a symlink:

update-alternatives --install /usr/bin/python python /usr/bin/python3 1

If you do not have Node.js v18 or higher installed, follow these steps to install Node.js v22:

# Update and install prerequisites
apt-get install -y curl gnupg ca-certificates

# Add NodeSource Node.js 22 repo
curl -fsSL https://deb.nodesource.com/setup_22.x | bash -

# Install Node.js 22
apt-get install -y nodejs

# Install Yarn package manager globally
npm install -g yarn

If your system doesn't have Conda, you can install it with:

wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/download/24.11.3-2/Miniforge3-24.11.3-2-Linux-x86_64.sh"
bash Miniforge3.sh -b -p "${HOME}/conda"

source "${HOME}/conda/etc/profile.d/conda.sh"
source "${HOME}/conda/etc/profile.d/mamba.sh"

All set to try the examples.