point to the Dockerfile in the docker folder instead

.gitlab-ci.yml

@@ -17,7 +17,7 @@ push_docker_image:
   stage: build
   image: docker:26.0.1-dind
   script:
-    - docker build -t $DOCKER_IMAGE:$CI_COMMIT_SHORT_SHA .
+    - docker build -t $DOCKER_IMAGE:$CI_COMMIT_SHORT_SHA -f docker/Dockerfile .
     - docker push $DOCKER_IMAGE:$CI_COMMIT_SHORT_SHA
   only:
     - main  # Only run on the main branch

Dockerfile

-# 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=12.2.2
-FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu20.04
-# FROM directive resets ARGS, so we specify again (the value is retained if
-# previously set).
-ARG CUDA
-
-# Use bash to support string substitution.
-SHELL ["/bin/bash", "-o", "pipefail", "-c"]
-
-RUN apt-get update \
-    && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
-        build-essential \
-        cmake \
-        cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
-        git \
-        hmmer \
-        kalign \
-        tzdata \
-        wget \
-    && rm -rf /var/lib/apt/lists/* \
-    && apt-get autoremove -y \
-    && apt-get clean
-
-# Compile HHsuite from source.
-RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
-    && mkdir /tmp/hh-suite/build \
-    && pushd /tmp/hh-suite/build \
-    && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
-    && make -j 4 && make install \
-    && ln -s /opt/hhsuite/bin/* /usr/bin \
-    && popd \
-    && rm -rf /tmp/hh-suite
-
-# Install Miniconda package manager.
-RUN wget -q -P /tmp \
-  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
-    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
-
-# Install conda packages.
-ENV PATH="/opt/conda/bin:$PATH"
-ENV LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
-RUN conda install -qy conda==24.1.2 pip python=3.11 \
-    && conda install -y -c nvidia cuda=${CUDA_VERSION} \
-    && conda install -y -c conda-forge openmm=8.0.0 pdbfixer \
-    && 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==0.4.26 \
-      jaxlib==0.4.26+cuda12.cudnn89 \
-      -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
-
-# Add SETUID bit to the ldconfig binary so that non-root users can run it.
-RUN chmod u+s /sbin/ldconfig.real
-
-# Currently needed to avoid undefined_symbol error.
-RUN ln -sf /usr/lib/x86_64-linux-gnu/libffi.so.7 /opt/conda/lib/libffi.so.7
-
-# 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"]
\ No newline at end of file