diff docker/claremcwhite/Dockerfile @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/claremcwhite/Dockerfile	Tue Mar 01 02:53:05 2022 +0000
@@ -0,0 +1,87 @@
+# 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_FULL=11.2.2
+FROM nvidia/cuda:${CUDA_FULL}-cudnn8-runtime-ubuntu20.04
+# FROM directive resets ARGS, so we specify again (the value is retained if
+# previously set).
+ARG CUDA_FULL
+ARG CUDA=11.2
+# JAXLIB no longer built for all minor CUDA versions:
+# https://github.com/google/jax/blob/main/CHANGELOG.md#jaxlib-0166-may-11-2021
+ARG CUDA_JAXLIB=11.1
+
+# Use bash to support string substitution.
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      build-essential \
+      cmake \
+      cuda-command-line-tools-${CUDA/./-} \
+      git \
+      hmmer \
+      kalign \
+      tzdata \
+      wget \
+    && rm -rf /var/lib/apt/lists/*
+
+# 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
+WORKDIR /tmp/hh-suite/build
+RUN cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
+    && make -j 4 && make install \
+    && ln -s /opt/hhsuite/bin/* /usr/bin \
+    && rm -rf /tmp/hh-suite
+
+# Install Miniconda package manger.
+RUN wget -q -P /tmp \
+  https://repo.anaconda.com/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh \
+    && bash /tmp/Miniconda3-py38_4.9.2-Linux-x86_64.sh -b -p /opt/conda \
+    && rm /tmp/Miniconda3-py38_4.9.2-Linux-x86_64.sh
+
+# Install conda packages.
+ENV PATH="/opt/conda/bin:$PATH"
+RUN conda update -qy conda \
+    && conda install -y -c conda-forge \
+      openmm=7.5.1 \
+      cudatoolkit==${CUDA_FULL} \
+      pdbfixer \
+      pip
+
+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 \
+    && pip3 install -r /app/alphafold/requirements.txt \
+    && pip3 install --upgrade jax jaxlib==0.1.69+cuda${CUDA_JAXLIB/./} -f \
+      https://storage.googleapis.com/jax-releases/jax_releases.html
+
+# Apply OpenMM patch.
+WORKDIR /opt/conda/lib/python3.8/site-packages
+RUN patch -p0 < /app/alphafold/docker/openmm.patch
+
+# 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"]