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QuickStart.md

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Quick Start

You will only need to run these steps once per Compute Canada user. The following instructions are meant to be a quickstart for installing TVB. If you come across any errors or unexpected outputs (e.g. one of the below python3 --version calls does not produce the expected output) then try the detailed installation here.

The below instructions assume that you have not installed TVB before.

Instructions

Perform the following with a clean, new Cedar session - do not load any modules before running these steps:

module reset
cd ~
mkdir TVB    # Assuming you don't already have a TVB install there. Otherwise, either delete the existing TVB install or use a different directory name for the rest of these steps. 
cd TVB
module load StdEnv/2020
python3 --version    # This should return 3.7.7
git clone https://github.com/ins-amu/virtual_aging_brain.git
cd virtual_aging_brain
python3   # To verify that you have python3 available
exit()
rm -rf env
python3 -m venv env
. env/bin/activate
pip3 install --upgrade pip
pip3 install wheel
pip3 install -r requirements.txt
pip3 install -e .
deactivate
cd ..

Obtain the virtual_ageing directory using steps 7 and 8 from Initial Setup on Compute Canada here.

cd virtual_ageing/ # You should be in ~/TVB/virtual_ageing
python3 --version   # This should return 3.7.7
module load scipy-stack/2023b
. ~/TVB/virtual_aging_brain/env/bin/activate    # Again, assuming your installation is in ~/TVB
python3 --version   # This should return 3.7.7
pip install --upgrade pip
pip install -e .
python3 --version   # This should return 3.7.7
mkdir -p ~/.local/share/jupyter/kernels
pip install --no-index ipykernel
python -m ipykernel install --user --name "PythonTVB" --display-name "PythonTVB"   # Assuming you have not created a PythonTVB kernel before. Use a new name if you have.