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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author galaxy-australia
date Tue, 01 Mar 2022 02:53:05 +0000
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6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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1 # Copyright 2021 DeepMind Technologies Limited
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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2 #
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3 # Licensed under the Apache License, Version 2.0 (the "License");
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4 # you may not use this file except in compliance with the License.
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5 # You may obtain a copy of the License at
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6 #
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7 # http://www.apache.org/licenses/LICENSE-2.0
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8 #
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9 # Unless required by applicable law or agreed to in writing, software
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10 # distributed under the License is distributed on an "AS IS" BASIS,
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11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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12 # See the License for the specific language governing permissions and
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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13 # limitations under the License.
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14
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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15 ARG CUDA_FULL=11.2.2
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16 FROM nvidia/cuda:${CUDA_FULL}-cudnn8-runtime-ubuntu20.04
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17 # FROM directive resets ARGS, so we specify again (the value is retained if
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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18 # previously set).
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19 ARG CUDA_FULL
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20 ARG CUDA=11.2
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21 # JAXLIB no longer built for all minor CUDA versions:
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22 # https://github.com/google/jax/blob/main/CHANGELOG.md#jaxlib-0166-may-11-2021
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23 ARG CUDA_JAXLIB=11.1
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24
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25 # Use bash to support string substitution.
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26 SHELL ["/bin/bash", "-c"]
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27
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28 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
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29 build-essential \
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30 cmake \
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31 cuda-command-line-tools-${CUDA/./-} \
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32 git \
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33 hmmer \
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34 kalign \
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35 tzdata \
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36 wget \
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37 && rm -rf /var/lib/apt/lists/*
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38
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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39 # Compile HHsuite from source.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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40 RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
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41 && mkdir /tmp/hh-suite/build
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42 WORKDIR /tmp/hh-suite/build
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43 RUN cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
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44 && make -j 4 && make install \
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45 && ln -s /opt/hhsuite/bin/* /usr/bin \
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46 && rm -rf /tmp/hh-suite
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47
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48 # Install Miniconda package manger.
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49 RUN wget -q -P /tmp \
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50 https://repo.anaconda.com/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh \
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51 && bash /tmp/Miniconda3-py38_4.9.2-Linux-x86_64.sh -b -p /opt/conda \
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52 && rm /tmp/Miniconda3-py38_4.9.2-Linux-x86_64.sh
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53
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54 # Install conda packages.
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55 ENV PATH="/opt/conda/bin:$PATH"
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56 RUN conda update -qy conda \
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57 && conda install -y -c conda-forge \
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58 openmm=7.5.1 \
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59 cudatoolkit==${CUDA_FULL} \
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60 pdbfixer \
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61 pip
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62
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63 COPY . /app/alphafold
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64 RUN wget -q -P /app/alphafold/alphafold/common/ \
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65 https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
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66
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67 # Install pip packages.
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68 RUN pip3 install --upgrade pip \
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69 && pip3 install -r /app/alphafold/requirements.txt \
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70 && pip3 install --upgrade jax jaxlib==0.1.69+cuda${CUDA_JAXLIB/./} -f \
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71 https://storage.googleapis.com/jax-releases/jax_releases.html
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72
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73 # Apply OpenMM patch.
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74 WORKDIR /opt/conda/lib/python3.8/site-packages
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75 RUN patch -p0 < /app/alphafold/docker/openmm.patch
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76
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77 # We need to run `ldconfig` first to ensure GPUs are visible, due to some quirk
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78 # with Debian. See https://github.com/NVIDIA/nvidia-docker/issues/1399 for
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79 # details.
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80 # ENTRYPOINT does not support easily running multiple commands, so instead we
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81 # write a shell script to wrap them up.
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82 WORKDIR /app/alphafold
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83 RUN echo $'#!/bin/bash\n\
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84 ldconfig\n\
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85 python /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh \
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86 && chmod +x /app/run_alphafold.sh
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
87 ENTRYPOINT ["/app/run_alphafold.sh"]