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Installation

BioPAP is a Python-based preprocessing pipeline that requires Python 3.10 or higher and Jupyter Notebook/Lab.

Choose One Installation Method

Select either the command-line method or the Anaconda method below, not both. Both will successfully install BioPAP and its requirements.

  • Command Line (Recommended): Standard development practice, easier to troubleshoot if issues occur
  • Anaconda: Simpler GUI-based approach for users unfamiliar with terminals

Install from Command Line

This method guides you through installing Python, pip, Jupyter, and BioPAP directly using terminal commands.

Step 1: Check Python and pip

Verify that Python 3.10+ and pip are installed:

python3 --version
pip3 --version

If not installed or version is too old, run:

sudo apt-get update
sudo apt-get install python3.11 python3-pip

Step 2: Install Jupyter Notebook

pip3 install notebook jupyter

Step 3: Install BioPAP

Clone the repository and install BioPAP in development mode:

git clone https://github.com/CentreForDigitalHumanities/BioPAP.git
cd BioPAP
pip3 install -e .

Step 4: Verify Installation

python3 --version
jupyter --version
python3 -c "import biopap; print(biopap.__version__)"

Step 1: Check Python and pip

Check if Python 3.10+ and pip are installed:

python3 --version
pip3 --version

If not installed, install using Homebrew:

brew update
brew install python@3.11

Step 2: Install Jupyter Notebook

pip3 install notebook jupyter

Step 3: Install BioPAP

Clone the repository and install BioPAP in development mode:

git clone https://github.com/CentreForDigitalHumanities/BioPAP.git
cd BioPAP
pip3 install -e .

Step 4: Verify Installation

python3 --version
jupyter --version
python3 -c "import biopap; print(biopap.__version__)"

Step 1: Check Python and pip

Open Command Prompt and verify Python 3.10+ and pip are installed:

python --version
pip --version

If not installed, download the installer from python.org. Important: During installation, check the box "Add Python to PATH".

After installation, verify in Command Prompt:

python --version
pip --version

Step 2: Install Jupyter Notebook

pip install notebook jupyter

Step 3: Install BioPAP

Clone the repository and install BioPAP in development mode:

git clone https://github.com/your-repo/BioPAP.git
cd BioPAP
pip install -e .

Step 4: Verify Installation

python --version
jupyter --version
python -c "import biopap; print(biopap.__version__)"

Install with Anaconda

Anaconda is a package manager with a graphical interface (Anaconda Navigator) that makes installation possible with minimal usage of the command line. Download it from the Anaconda website.

Step 1: Install Anaconda

  1. Download the Anaconda installer and run it.
  2. Follow the installer prompts and accept the defaults.
  3. Close and reopen your terminal when finished.

Step 2: Open Anaconda Navigator

  1. Search for "Anaconda Navigator" in your applications menu and open it.
  2. Wait for it to load (this might take a minute).

Step 3: Install Jupyter

  1. In Anaconda Navigator, look for "Jupyter Notebook" in the home tab.
  2. Click the Launch button next to Jupyter Notebook.
  3. Jupyter will open in your web browser.

Step 4: Install BioPAP

  1. Open a terminal and navigate to where you want to store BioPAP: 
    git clone https://github.com/your-repo/BioPAP.git
cd BioPAP
pip install -e .

Step 5: Open the Example Notebook

  1. In Jupyter (which should still be open in your browser), navigate to the BioPAP folder you just cloned.
  2. Open the folder: examples
  3. Click on pipeline.ipynb to open the example notebook.
  4. You're ready to start using BioPAP!

Step 1: Install Anaconda

  1. Download and run the Anaconda installer.
  2. Follow the installer prompts with default settings.
  3. Close and reopen your terminal when finished.

Step 2: Open Anaconda Navigator

  1. Look for "Anaconda Navigator" in your Applications folder and open it.
  2. Wait for it to load (this might take a minute).

Step 3: Install Jupyter

  1. In Anaconda Navigator, find "Jupyter Notebook" in the home tab.
  2. Click the Launch button next to Jupyter Notebook.
  3. Jupyter will open in your web browser.

Step 4: Install BioPAP

  1. Open a terminal and navigate to where you want to store BioPAP: 
    git clone https://github.com/your-repo/BioPAP.git
cd BioPAP
pip install -e .

Step 5: Open the Example Notebook

  1. In Jupyter (which should still be open in your browser), navigate to the BioPAP folder you just cloned.
  2. Open the folder: examples
  3. Click on pipeline.ipynb to open the example notebook.
  4. You're ready to start using BioPAP!

Step 1: Install Anaconda

  1. Download the Anaconda installer (.exe) and double-click to run it.
  2. Follow the installer steps with default settings.
  3. Important: Check the box "Register Anaconda3 as my default Python 3.x" at the Advanced Installation Options.
  4. Close and reopen Command Prompt when finished.

Step 2: Open Anaconda Navigator

  1. Click the Start menu and search for "Anaconda Navigator".
  2. Click to open Anaconda Navigator.
  3. Wait for it to load (this might take a minute).

Step 3: Install Jupyter

  1. In Anaconda Navigator, find "Jupyter Notebook" in the home tab.
  2. Click the Launch button next to Jupyter Notebook.
  3. Jupyter will open in your web browser.

Step 4: Install BioPAP

  1. Open Command Prompt and navigate to where you want to store BioPAP: 
    git clone https://github.com/your-repo/BioPAP.git
cd BioPAP
pip install -e .

Step 5: Open the Example Notebook

  1. In Jupyter (which should still be open in your browser), navigate to the BioPAP folder you just cloned.
  2. Open the folder: examples
  3. Click on pipeline.ipynb to open the example notebook.
  4. You're ready to start using BioPAP!

Next Steps