mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-06 15:40:14 +08:00
87 lines
2.9 KiB
Docker
87 lines
2.9 KiB
Docker
# 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.
|
|
|
|
# Extended by Valentin Maurer <valentin.maurer@embl-hamburg.de>
|
|
|
|
ARG CUDA=11.8.0
|
|
FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu20.04
|
|
ARG CUDA
|
|
|
|
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
|
|
RUN apt update -y && apt upgrade -y
|
|
RUN apt install -y --reinstall libp11-kit0 libffi7
|
|
RUN apt-get update \
|
|
&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
|
|
build-essential \
|
|
cmake \
|
|
cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
|
|
hmmer \
|
|
kalign \
|
|
tzdata \
|
|
wget \
|
|
bc \
|
|
&& rm -rf /var/lib/apt/lists/* \
|
|
&& apt-get autoremove -y \
|
|
&& apt-get clean
|
|
|
|
RUN wget -q -P /tmp \
|
|
https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
|
|
&& bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
|
|
&& rm /tmp/Miniconda3-latest-Linux-x86_64.sh
|
|
ENV PATH="/opt/conda/bin:$PATH"
|
|
ENV LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
|
|
|
|
RUN conda install conda-forge::git
|
|
|
|
RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
|
|
&& mkdir /tmp/hh-suite/build \
|
|
&& pushd /tmp/hh-suite/build \
|
|
&& cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
|
|
&& make -j 4 && make install \
|
|
&& ln -s /opt/hhsuite/bin/* /usr/bin \
|
|
&& popd \
|
|
&& rm -rf /tmp/hh-suite
|
|
|
|
RUN conda install -y -c conda-forge -c bioconda --solver classic \
|
|
openmm==8.0 \
|
|
cudatoolkit==${CUDA_VERSION} \
|
|
pdbfixer==1.9 \
|
|
cctbx-base \
|
|
kalign2 \
|
|
importlib_metadata \
|
|
modelcif \
|
|
pip \
|
|
python=3.10 \
|
|
&& conda clean --all --force-pkgs-dirs --yes
|
|
|
|
RUN conda install -y -c nvidia cuda-nvcc --solver classic
|
|
|
|
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
|
|
|
|
RUN pip3 install git+https://github.com/KosinskiLab/AlphaPulldown.git@main
|
|
|
|
RUN pip3 install --upgrade pip --no-cache-dir \
|
|
&& pip3 install --upgrade --no-cache-dir \
|
|
-i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple \
|
|
pytest \
|
|
jax==0.4.23 \
|
|
jaxlib==0.4.23+cuda11.cudnn86 \
|
|
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
|
|
|
|
RUN chmod u+s /sbin/ldconfig.real
|
|
|
|
ENTRYPOINT ["bash"]
|