Mercurial > repos > goeckslab > extract_embeddings
diff Docker/Dockerfile @ 1:84f96c952c2c draft default tip
planemo upload for repository https://github.com/goeckslab/gleam.git commit 5b6cd961948137853177b14b0fff80a5d40e8a07
| author | goeckslab |
|---|---|
| date | Sun, 09 Nov 2025 19:03:21 +0000 |
| parents | 38333676a029 |
| children |
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--- a/Docker/Dockerfile Thu Jun 19 23:33:23 2025 +0000 +++ b/Docker/Dockerfile Sun Nov 09 19:03:21 2025 +0000 @@ -1,21 +1,48 @@ -# Use a lightweight Python 3.9 base image -FROM python:3.9-slim +# Use NVIDIA CUDA base image for GPU support +FROM nvidia/cuda:11.8-devel-ubuntu20.04 -# Install system dependencies for OpenCV and other libraries in one layer +# Set environment variables +ENV DEBIAN_FRONTEND=noninteractive +ENV PYTHONUNBUFFERED=1 + +# Install system dependencies RUN apt-get update && apt-get install -y \ + python3 \ + python3-pip \ + python3-dev \ libgl1-mesa-glx \ libglib2.0-0 \ + git \ + wget \ && rm -rf /var/lib/apt/lists/* -# Upgrade pip to the latest version +# Create symbolic links for python +RUN ln -s /usr/bin/python3 /usr/bin/python && \ + ln -s /usr/bin/pip3 /usr/bin/pip + +# Upgrade pip RUN pip install --upgrade pip -# Install PyTorch and torchvision CPU-only versions +# Install PyTorch with CUDA support RUN pip install --no-cache-dir torch==2.0.0 torchvision==0.15.1 \ - -f https://download.pytorch.org/whl/cpu/torch_stable.html + -f https://download.pytorch.org/whl/cu118/torch_stable.html # Install NumPy with a version compatible with PyTorch 2.0.0 RUN pip install --no-cache-dir numpy==1.24.4 -# Install remaining Python dependencies -RUN pip install --no-cache-dir Pillow opencv-python pandas fastparquet argparse logging multiprocessing +# Install timm for model support (quote to prevent shell redirection) +RUN pip install --no-cache-dir 'timm>=1.0.3' + +# Install remaining Python dependencies (exclude stdlib packages, add requests for GPFM) +RUN pip install --no-cache-dir Pillow opencv-python pandas fastparquet requests + +# Install HuggingFace transformers for model loading +RUN pip install --no-cache-dir transformers huggingface-hub + +# Set working directory +WORKDIR /workspace + +# Create cache directory for HuggingFace models +RUN mkdir -p /workspace/hf_cache +ENV HF_HOME=/workspace/hf_cache +ENV TORCH_HOME=/workspace/hf_cache
