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Update setup script
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adjavon committed Aug 16, 2024
1 parent c1a6e28 commit 559ccf9
Showing 1 changed file with 3 additions and 21 deletions.
24 changes: 3 additions & 21 deletions setup.sh
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#!/usr/bin/env -S bash -i
echo "Creating conda environment"
mamba env create -f environment.yaml

# get the CycleGAN code and dependencies
git clone https://github.com/funkey/neuromatch_xai
mv neuromatch_xai/cycle_gan .
rm -rf neuromatch_xai

# Download checkpoints and data
wget 'https://dl-at-mbl-2023-data.s3.us-east-2.amazonaws.com/knowledge_extraction_resources.zip' -O resources.zip
# Unzip the checkpoints and data
unzip -o resources.zip data.zip
unzip -o resources.zip checkpoints.zip
unzip -o checkpoints.zip 'checkpoints/synapses/*'
unzip -o data.zip 'data/raw/synapses/*'
# make sure the order of classes matches the pretrained model
mv data/raw/synapses/gaba data/raw/synapses/0_gaba
mv data/raw/synapses/acetylcholine data/raw/synapses/1_acetylcholine
mv data/raw/synapses/glutamate data/raw/synapses/2_glutamate
mv data/raw/synapses/serotonin data/raw/synapses/3_serotonin
mv data/raw/synapses/octopamine data/raw/synapses/4_octopamine
mv data/raw/synapses/dopamine data/raw/synapses/5_dopamine
mamba create -n 08_knowledge_extraction python=3.11 pytorch torchvision pytorch-cuda-12.1 -c conda-forge -c pytorch -c nvidia
mamba activate 08_knowledge_extraction
pip install -r requirements.txt

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