File size: 1,725 Bytes
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Download scGPT whole-human pretrained model.
Run on login node: python scripts/download_scgpt.py
"""
import os
import sys
def download_scgpt_model(output_dir: str = "transfer/data/scGPT_pretrained"):
"""Download scGPT whole-human model files."""
os.makedirs(output_dir, exist_ok=True)
required_files = ["best_model.pt", "vocab.json", "args.json"]
missing = [f for f in required_files if not os.path.exists(os.path.join(output_dir, f))]
if not missing:
print(f"All scGPT pretrained files already exist in {output_dir}")
return
print(f"Missing files: {missing}")
print(f"Please download the scGPT whole-human pretrained model to: {output_dir}")
print()
print("Option 1: From the scGPT release (if available):")
print(" Download from: https://github.com/bowang-lab/scGPT/releases")
print(f" Place files in: {output_dir}/")
print()
print("Option 2: Manual setup:")
print(" Required files:")
for f in required_files:
print(f" - {f}")
print()
print(" args.json example content:")
print(' {"embsize": 512, "nheads": 8, "d_hid": 512, "nlayers": 12,')
print(' "n_layers_cls": 3, "dropout": 0.2, "pad_token": "<pad>",')
print(' "pad_value": 0, "mask_value": -1}')
if __name__ == "__main__":
# Default path relative to repo root
repo_root = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
default_dir = os.path.join(repo_root, "data", "scGPT_pretrained")
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--output_dir", default=default_dir)
args = parser.parse_args()
download_scgpt_model(args.output_dir)
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