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FROM ai4s-cn-beijing.cr.volces.com/pytorch-mirror/pytorch:2.3.1-cuda12.1-cudnn8-devel
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ=Asia/Shanghai
RUN apt-get update && \
apt-get install -y --no-install-recommends \
wget \
g++ \
gcc \
libc6-dev \
make zlib1g zlib1g-dev \
git git-lfs expect zsh vim wget curl unzip zip cmake cmake-curses-gui libgdbm-dev libnss3-dev libssl-dev libreadline-dev libffi-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN apt update && apt -y install postgresql
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
hmmer cmake cmake-curses-gui \
&& git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
&& mkdir /tmp/hh-suite/build \
&& cd /tmp/hh-suite/build \
&& cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
&& make -j 32 && make install \
&& ln -s /opt/hhsuite/bin/* /usr/bin \
&& cd - \
&& rm -rf /tmp/hh-suite
RUN apt-get install -yq --no-install-recommends iproute2 curl
# Add PIP Package
RUN pip3 --no-cache-dir install \
scipy \
ml_collections \
tqdm \
pandas \
optree \
rdkit
# Add openfold dependency
RUN pip3 --no-cache-dir install \
biopython==1.83 \
modelcif==0.7
# Add datapipeline dependency
RUN pip3 --no-cache-dir install \
biotite==1.0.1 \
scikit-learn \
scikit-learn-extra \
fair-esm \
deepspeed \
protobuf==3.20.2 tos icecream ipdb wandb numpy==1.26.3 matplotlib==3.9.2 ipywidgets py3Dmol
# For H20 compatibility
RUN pip3 install --no-cache-dir nvidia-cublas-cu12==12.4.5.8 --no-deps
RUN git clone -b v3.5.1 https://github.com/NVIDIA/cutlass.git /opt/cutlass
ENV CUTLASS_PATH=/opt/cutlass
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