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Add conda env #42

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Add conda env #42

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6398ea2
Add phenomix
bschilder May 24, 2024
2316d02
Add gitignore
bschilder May 24, 2024
48ace33
update jupyter notebook
bschilder May 24, 2024
337b7b5
add conda env
bschilder Jun 3, 2024
cdebf33
add conda env
bschilder Jun 3, 2024
ce558ec
Revert "Update new_species_protein_embeddings.csv"
bschilder Jun 3, 2024
e06e999
Merge branch 'main' of https://github.com/bschilder/UCE into HEAD
bschilder Jun 3, 2024
2de7c56
rm gitignore
bschilder Jun 3, 2024
191320e
update conda env
bschilder Jun 3, 2024
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27 changes: 27 additions & 0 deletions conda.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
name: uce
channels:
- conda-forge
- pytorch
- nvidia
- defaults
dependencies:
- python
- pandas
- scikit-learn
- numpy
- tqdm
- pytorch>=2.0.0
- pytorch-gpu
- torchvision
- torchaudio
- cuda-toolkit>=12.0.0
- accelerate
- requests
- urllib3==1.26.6
- scanpy
# - python-igraph
# - leidenalg
- ipykernel
- pip
- pip:
- gdown
1 change: 1 addition & 0 deletions model_files/new_species_protein_embeddings.csv
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@@ -1 +1,2 @@
species,path
chicken,/dfs/project/cross-species/yanay/code/uce_code/UCE_public/model_files/protein_embeddings/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.pep.all.gene_symbol_to_embedding_ESM2.pt