mirror of
https://github.com/google-deepmind/alphafold.git
synced 2026-06-04 14:58:05 +08:00
91 lines
3.2 KiB
Docker
91 lines
3.2 KiB
Docker
# Copyright 2021 DeepMind Technologies Limited
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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ARG CUDA=11.1.1
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FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu18.04
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# FROM directive resets ARGS, so we specify again (the value is retained if
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# previously set).
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ARG CUDA
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# Use bash to support string substitution.
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SHELL ["/bin/bash", "-c"]
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RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
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build-essential \
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cmake \
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cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
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git \
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hmmer \
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kalign \
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tzdata \
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wget \
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&& rm -rf /var/lib/apt/lists/*
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# Compile HHsuite from source.
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RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
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&& mkdir /tmp/hh-suite/build \
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&& pushd /tmp/hh-suite/build \
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&& cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
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&& make -j 4 && make install \
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&& ln -s /opt/hhsuite/bin/* /usr/bin \
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&& popd \
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&& rm -rf /tmp/hh-suite
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# Install Miniconda package manager.
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RUN wget -q -P /tmp \
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https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
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&& rm /tmp/Miniconda3-latest-Linux-x86_64.sh
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# Install conda packages.
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ENV PATH="/opt/conda/bin:$PATH"
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RUN conda update -qy conda \
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&& conda install -y -c conda-forge \
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openmm=7.5.1 \
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cudatoolkit==${CUDA_VERSION} \
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pdbfixer \
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pip \
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python=3.7
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COPY . /app/alphafold
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RUN wget -q -P /app/alphafold/alphafold/common/ \
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https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
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# Install pip packages.
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RUN pip3 install --upgrade pip \
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&& pip3 install -r /app/alphafold/requirements.txt \
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&& pip3 install --upgrade \
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jax==0.2.14 \
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jaxlib==0.1.69+cuda$(cut -f1,2 -d. <<< ${CUDA} | sed 's/\.//g') \
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-f https://storage.googleapis.com/jax-releases/jax_releases.html
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# Apply OpenMM patch.
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WORKDIR /opt/conda/lib/python3.7/site-packages
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RUN patch -p0 < /app/alphafold/docker/openmm.patch
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# Add SETUID bit to the ldconfig binary so that non-root users can run it.
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RUN chmod u+s /sbin/ldconfig.real
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# We need to run `ldconfig` first to ensure GPUs are visible, due to some quirk
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# with Debian. See https://github.com/NVIDIA/nvidia-docker/issues/1399 for
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# details.
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# ENTRYPOINT does not support easily running multiple commands, so instead we
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# write a shell script to wrap them up.
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WORKDIR /app/alphafold
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RUN echo $'#!/bin/bash\n\
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ldconfig\n\
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python /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh \
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&& chmod +x /app/run_alphafold.sh
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ENTRYPOINT ["/app/run_alphafold.sh"]
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