mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 22:34:26 +08:00
62 lines
1.8 KiB
Docker
62 lines
1.8 KiB
Docker
# syntax = docker/dockerfile:1.4
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ARG CUDA=12.2.2
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FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu20.04
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ARG CUDA
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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RUN apt update -y && apt upgrade -y
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RUN apt install -y --reinstall libp11-kit0 libffi7
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RUN apt-get update \
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&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
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build-essential \
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cmake \
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cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
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tzdata \
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wget \
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bc \
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openssh-client \
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&& rm -rf /var/lib/apt/lists/* \
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&& apt-get autoremove -y \
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&& apt-get clean
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RUN wget -q -P /tmp https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
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&& bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
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&& rm /tmp/Miniforge3-Linux-x86_64.sh
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ENV PATH="/opt/conda/bin:$PATH"
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ENV LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
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RUN conda install --solver=classic -y \
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conda-forge::conda-libmamba-solver \
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conda-forge::libmamba \
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conda-forge::libmambapy \
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conda-forge::libarchive \
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conda-forge::git
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RUN mamba install -y -c conda-forge -c bioconda -c omnia \
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openmm==8.0 \
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pdbfixer==1.9 \
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kalign2 \
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modelcif \
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pip \
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hmmer \
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hhsuite \
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python=3.10 \
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&& conda clean --all --force-pkgs-dirs --yes
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RUN mkdir -p /root/.ssh && chmod 700 /root/.ssh
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RUN ssh-keyscan github.com >> /root/.ssh/known_hosts
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RUN git clone --recurse-submodules https://github.com/KosinskiLab/AlphaPulldown.git
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#COPY . /AlphaPulldown
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WORKDIR AlphaPulldown
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RUN pip3 install .
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RUN pip3 install --upgrade pip --no-cache-dir \
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&& pip3 install --upgrade --no-cache-dir \
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pytest \
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"jax[cuda12]"==0.5.3
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RUN chmod u+s /sbin/ldconfig.real
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ENTRYPOINT ["bash"]
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