Step 1. Update your system

Open your terminal and run the following command to update your system:

sudo apt update && sudo apt upgrade -y
Step 2. Install Python and required tools
ScientiFlow requires Python 3 and a few essential utilities.
You can install everything safely in one command — if already installed, it will be skipped automatically.
sudo apt install -y python3 python3-pip python3-venv pipx
After installation, verify Python and pipx are available:
python3 --version
pipx --version
Then ensure pipx is on your system path:
pipx ensurepath
source ~/.bashrc
Step 3. Install ScientiFlow CLI
Now install the ScientiFlow command-line tool:
pipx install scientiflow-cli
Once done, verify the installation:
scientiflow-cli --help
You should see a help menu listing available commands.
Step 4. Set up Singularity
To enable containerized workflows, install and configure Singularity directly using the CLI:
For CPU-based systems:
scientiflow-cli --install-singularity
For GPU-based systems (recommended for simulations):
scientiflow-cli --install-singularity --enable-gpu
This command automatically installs:
Singularity.
NVIDIA Container Toolkit (for GPU acceleration).
All other required dependencies. 
No manual setup needed.
Step 5. Verify Installation
After setup, confirm that everything is working:
singularity --version
scientiflow-cli --version
You are now ready to run and manage your scientific workflows using ScientiFlow