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HPC Installation Instructions #127

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33 changes: 33 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,39 @@ Once you are ready, you can save your file:
pipeline.save(pipeline.get_derivative_path(bids_path), overwrite=True)
```

## ▶️ Example HPC Environment Setup

Assuming you are on a system such as [Narval](https://docs.alliancecan.ca/wiki/Narval/en):

```bash
module load python/3.10

# Build the virtualenv in your homedir
virtualenv --no-download eeg-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 mne_bids

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the user also needs to pip install edflib-python for full lossless functionality (saving).

# Clone down mne-iclabel and switch to the right version and install it locally
git clone https://github.com/mne-tools/mne-icalabel.git
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Out of curiosity - is it necessary to checkout a certain branch of mne-icalabel?

cd mne-icalabel
git checkout maint/0.4
pip install .

# Clone down pipeline and install without reading dependencies
git clone [email protected]:lina-usc/pylossless.git
cd pylossless
pip install --no-deps .

# Verify that the package has installed correct with an import
python -c 'import pylossless'
```

## 👩‍💻 Dashboard Review
[![Open in Colab](https://camo.githubusercontent.com/84f0493939e0c4de4e6dbe113251b4bfb5353e57134ffd9fcab6b8714514d4d1/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667)](https://colab.research.google.com/github/lina-usc/pylossless/blob/main/notebooks/qc_example.ipynb)

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