Load required modules

module load python/3.10

navigate to the pylossless derivative directory

cd /project/def-emayada/q1k/pilot/q1k-external-pilot/derivatives/pylossless/code

Download the repo

git clone https://github.com/lina-usc/q1k_submit_pylossless.com

Navigate into the repo dirctory and install the tools

cd q1k_submit_pylossless

virtualenv --no-download env
source eeg-env/bin/activate

pip install --no-index mne
pip install --no-index pandas
pip install --no-index xarray
pip install --no-index pyyaml
pip install --no-index sklearn
pip install EDFlib-Python
pip install edfio
pip install onnxruntime
pip install openneuro-py
pip install mne_bids

Clone down mne-iclabel and switch to the right version and install it locally

git clone https://github.com/mne-tools/mne-icalabel.git
cd mne-icalabel
git checkout maint/0.4
pip install .
cd ..

Clone down pipeline and install without reading dependencies

git clone [email protected]:lina-usc/pylossless.git
cd pylossless
pip install --no-deps .
cd ..

usage:

source env/bin/activate
sbatch q1k_yll_jobsub.sh /project/def-emayada/q1k/pilot/q1k-external-pilot/ 002 01 mn 1 /project/def-emayada/q1k/pilot/q1k-external-pilot