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HPC Installation Instructions #127
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@@ -56,6 +56,39 @@ Once you are ready, you can save your file: | |
pipeline.save(pipeline.get_derivative_path(bids_path), overwrite=True) | ||
``` | ||
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## ▶️ Example HPC Environment Setup | ||
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Assuming you are on a system such as [Narval](https://docs.alliancecan.ca/wiki/Narval/en): | ||
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```bash | ||
module load python/3.10 | ||
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# Build the virtualenv in your homedir | ||
virtualenv --no-download eeg-env | ||
source eeg-env/bin/activate | ||
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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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# Clone down mne-iclabel and switch to the right version and install it locally | ||
git clone https://github.com/mne-tools/mne-icalabel.git | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Out of curiosity - is it necessary to checkout a certain branch of mne-icalabel? |
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cd mne-icalabel | ||
git checkout maint/0.4 | ||
pip install . | ||
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# Clone down pipeline and install without reading dependencies | ||
git clone [email protected]:lina-usc/pylossless.git | ||
cd pylossless | ||
pip install --no-deps . | ||
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# Verify that the package has installed correct with an import | ||
python -c 'import pylossless' | ||
``` | ||
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## 👩💻 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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the user also needs to
pip install edflib-python
for full lossless functionality (saving).