Mercurial > repos > goeckslab > extract_embeddings
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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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# Use NVIDIA CUDA base image for GPU support FROM nvidia/cuda:11.8-devel-ubuntu20.04 # 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/* # 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 with CUDA support RUN pip install --no-cache-dir torch==2.0.0 torchvision==0.15.1 \ -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 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
