diff --git a/conda.yml b/conda.yml new file mode 100644 index 0000000..6043fe9 --- /dev/null +++ b/conda.yml @@ -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 diff --git a/model_files/new_species_protein_embeddings.csv b/model_files/new_species_protein_embeddings.csv index 5d134d1..c3eb19f 100644 --- a/model_files/new_species_protein_embeddings.csv +++ b/model_files/new_species_protein_embeddings.csv @@ -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 \ No newline at end of file