From 559ccf9e44053f2dd0922120a3f4eaec6de2f138 Mon Sep 17 00:00:00 2001 From: Diane Adjavon Date: Fri, 16 Aug 2024 11:27:29 -0400 Subject: [PATCH] Update setup script --- setup.sh | 24 +++--------------------- 1 file changed, 3 insertions(+), 21 deletions(-) diff --git a/setup.sh b/setup.sh index 12ce1a1..12bc849 100755 --- a/setup.sh +++ b/setup.sh @@ -1,23 +1,5 @@ #!/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 \ No newline at end of file