Getting Started¶

Install WSL

To run ImputeGAP in a Unix-compatible environment on Windows, install the Windows Subsystem for Linux (WSL).

1. Search for WSL in the Start menu to check if it’s already installed.

2. If not, open PowerShell as Administrator.

3. Run the following command:

wsl --install

4. Restart your computer once the installation completes.

Prepare Python 3.12 Environment

To ensure a proper Python setup, we recommend creating a dedicated Python environment for the project. Python 3.12 is a suitable and supported choice.

Step 1: Check Existing Python Version

Open your terminal and check the currently installed version of Python:

python3 --version

Step 2: Install Python 3.12

If needed, install Python 3.12 on your WSL system, follow these steps:

1. Update your package list and install prerequisites:

sudo apt-get update
sudo apt install -y build-essential libssl-dev zlib1g-dev libncurses5-dev libncursesw5-dev \
libreadline-dev libsqlite3-dev libgdbm-dev libdb5.3-dev libbz2-dev libexpat1-dev liblzma-dev \
tk-dev python3-tk libopenblas0 libarmadillo-dev software-properties-common python3-pip

3. Add the deadsnakes PPA and update:

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update

4. Install Python 3.12:

sudo apt-get install python3.12 python3.12-venv python3.12-dev

5. Verify the installation:

python3.12 --version

Install Python 3.12 Environment

1. Create a virtual environment:

python3.12 -m venv imputegap_env

2. Activate the virtual environment:

source imputegap_env/bin/activate

3. Install ImputeGAP

pip install imputegap

Prepare Python 3.12 Environment

To ensure a proper Python setup, we recommend creating a dedicated Python environment for the project. Python 3.12 is a suitable and supported choice.

Step 1: Check Existing Python Version*

Open your terminal and check the currently installed version of Python:

python3 --version

*Step 2: Install Python 3.12

If needed, install Python 3.12 on your system, follow these steps:

1. Update your package list and install prerequisites:

sudo apt-get update

sudo apt install -y build-essential libssl-dev zlib1g-dev libncurses5-dev libncursesw5-dev \
libreadline-dev libsqlite3-dev libgdbm-dev libdb5.3-dev libbz2-dev libexpat1-dev liblzma-dev \
tk-dev python3-tk libopenblas0 libarmadillo-dev software-properties-common python3-pip

3. Add the deadsnakes PPA and update:

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update

4. Install Python 3.12:

sudo apt-get install python3.12 python3.12-venv python3.12-dev

5. Verify the installation:

python3.12 --version

Install Python 3.12 Environment

1. Create a virtual environment:

python3.12 -m venv imputegap_env

2. Activate the virtual environment:

source imputegap_env/bin/activate

3. Install ImputeGAP

pip install imputegap

Prepare Python 3.12 Environment

To ensure a proper Python setup, we recommend creating a dedicated Python environment for the project. Python 3.12 is a suitable and supported choice.

1. Install Xcode Command Line Tools (required by Homebrew):

xcode-select --install

2. Install Homebrew (if not already installed):

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

3. Update Homebrew, install prerequisites, and install Python 3.12:

brew update
brew install openssl zlib ncurses readline sqlite gdbm berkeley-db@5 bzip2 expat xz tcl-tk openblas armadillo python@3.12 python-tk@3.12

4. Verify the installation:

python3.12 --version

Install Python 3.12 Environment

1. Create a virtual environment:

python3.12 -m venv imputegap_env

2. Activate the virtual environment:

source imputegap_env/bin/activate

3. Install ImputeGAP

pip install imputegap

4. ⚠️ Warning

Depending on your macOS security settings, you may need to manually approve the C++ wrapper library (.dylib file) in System Settings → Privacy & Security before it can be loaded.

Launch Docker from desktop of terminal. To make sure it is running:

docker version

Pull the ImputeGAP Docker image:

docker pull qnater/imputegap:1.1.21

Run the Docker container:

docker run -p 8888:8888 qnater/imputegap:1.1.21

Open the following link:

http://127.0.0.1:8888

Launch Docker from desktop of terminal. To make sure it is running:

docker version

Pull the ImputeGAP Docker image:

docker pull qnater/imputegap:1.1.21

Run the Docker container:

docker run -p 8888:8888 qnater/imputegap:1.1.21

Open the following link:

http://127.0.0.1:8888

Launch Docker from desktop of terminal. To make sure it is running:

docker version

Pull the ImputeGAP Docker image:

docker pull --platform linux/x86_64 qnater/imputegap:1.1.21

Run the Docker container:

docker run -p 8888:8888 qnater/imputegap:1.1.21

Open the following link:

http://127.0.0.1:8888