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Dockerfile
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FROM pytorch/pytorch:2.0.0-cuda11.7-cudnn8-runtime
# Update and install dependencies
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install wget bzip2 ca-certificates curl git ffmpeg libsm6 libxext6 -y
# # Download and install Miniconda
# ENV CONDA_AUTO_UPDATE_CONDA=false
# RUN wget -q https://repo.anaconda.com/miniconda/Miniconda3-py38_23.1.0-1-Linux-x86_64.sh -O ~/miniconda.sh \
# && /bin/bash ~/miniconda.sh -b -p /opt/conda \
# && rm ~/miniconda.sh \
# # && /opt/conda/bin/conda clean -all \
# && ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
# && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
# && echo "conda activate base" >> ~/.bashrc
# ENV PATH=/opt/conda/bin:$PATH
# Install scSLAT
# RUN echo "conda activate base" >> ~/.bashrc
# RUN conda install -c conda-forge -y mamba
# RUN mamba install -c conda-forge -c bioconda snakemake==7.12.0 tabulate==0.8.10 -y
RUN pip3 install --upgrade pip
RUN git clone https://github.com/gao-lab/SLAT \
&& cd SLAT && pip install -e ".[dev, docs]" \
&& pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cu117.html