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# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
ARG CUDA=11.1.1
FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu18.04
# FROM directive resets ARGS, so we specify again (the value is retained if
# previously set).
ARG CUDA
# Use bash to support string substitution.
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
build-essential \
cmake \
cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
git \
hmmer \
kalign \
tzdata \
wget \
&& rm -rf /var/lib/apt/lists/* \
&& apt-get autoremove -y \
&& apt-get clean
# Compile HHsuite from source.
RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
&& mkdir /tmp/hh-suite/build \
&& pushd /tmp/hh-suite/build \
&& cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
&& make -j 4 && make install \
&& ln -s /opt/hhsuite/bin/* /usr/bin \
&& popd \
&& rm -rf /tmp/hh-suite
# Install Miniconda package manager.
RUN wget -q -P /tmp \
Matthew K Defenderfer
committed
https://repo.anaconda.com/miniconda/Miniconda3-py38_23.11.0-2-Linux-x86_64.sh \
&& bash /tmp/Miniconda3-py38_23.11.0-2-Linux-x86_64.sh -b -p /opt/conda \
&& rm /tmp/Miniconda3-py38_23.11.0-2-Linux-x86_64.sh
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# Install conda packages.
ENV PATH="/opt/conda/bin:$PATH"
RUN conda install -qy conda==4.13.0 \
&& conda install -y -c conda-forge \
openmm=7.5.1 \
cudatoolkit==${CUDA_VERSION} \
pdbfixer \
pip \
python=3.8 \
&& conda clean --all --force-pkgs-dirs --yes
COPY . /app/alphafold
RUN wget -q -P /app/alphafold/alphafold/common/ \
https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
# Install pip packages.
RUN pip3 install --upgrade pip --no-cache-dir \
&& pip3 install -r /app/alphafold/requirements.txt --no-cache-dir \
&& pip3 install --upgrade --no-cache-dir \
jax==0.3.25 \
jaxlib==0.3.25+cuda11.cudnn805 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
# Apply OpenMM patch.
WORKDIR /opt/conda/lib/python3.8/site-packages
RUN patch -p0 < /app/alphafold/docker/openmm.patch
# Add SETUID bit to the ldconfig binary so that non-root users can run it.
RUN chmod u+s /sbin/ldconfig.real
# We need to run `ldconfig` first to ensure GPUs are visible, due to some quirk
# with Debian. See https://github.com/NVIDIA/nvidia-docker/issues/1399 for
# details.
# ENTRYPOINT does not support easily running multiple commands, so instead we
# write a shell script to wrap them up.
WORKDIR /app/alphafold
RUN echo $'#!/bin/bash\n\
ldconfig\n\
python /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh \
&& chmod +x /app/run_alphafold.sh
ENTRYPOINT ["/app/run_alphafold.sh"]