mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-11-04 22:25:42 +00:00
71 lines
2.9 KiB
Docker
71 lines
2.9 KiB
Docker
FROM mambaorg/micromamba:1.5.0 as micromamba
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FROM nvidia/cuda:11.8.0-base-ubuntu22.04
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ARG DEBIAN_FRONTEND=noninteractive
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# Create root owned env: https://github.com/mamba-org/micromamba-docker/blob/main/examples/add_micromamba/Dockerfile
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USER root
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ENV MAMBA_USER=root
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ENV MAMBA_USER_ID=0
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ENV MAMBA_USER_GID=0
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ENV MAMBA_ROOT_PREFIX="/opt/conda"
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ENV MAMBA_EXE="/bin/micromamba"
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COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
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COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
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COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
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COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
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COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
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COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
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RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
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/usr/local/bin/_dockerfile_setup_root_prefix.sh
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SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
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ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
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# Install system dependencies
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RUN apt-get update && apt-get install -y \
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aria2 \
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build-essential \
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curl \
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git \
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tar \
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wget \
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unzip \
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vim \
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&& rm -rf /var/lib/apt/lists/* \
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&& micromamba install --name base -y python=3.11 -c conda-forge \
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&& micromamba clean --all --yes
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# DPF: everything below this line will have micromamba env activated
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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WORKDIR /opt
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ADD . /opt/RoseTTAFold-All-Atom/
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RUN pip --no-cache-dir install -e ./RoseTTAFold-All-Atom/rf2aa/SE3Transformer --no-deps
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WORKDIR /opt/RoseTTAFold-All-Atom
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ADD install_dependencies.sh /opt/RoseTTAFold-All-Atom/install_dependencies.sh
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RUN bash /opt/RoseTTAFold-All-Atom/install_dependencies.sh
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RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz
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RUN mkdir -p blast-2.2.26
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RUN tar -xf blast-2.2.26-x64-linux.tar.gz -C blast-2.2.26
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RUN cp -r blast-2.2.26/blast-2.2.26/ blast-2.2.26_bk
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RUN rm -r blast-2.2.26
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RUN mv blast-2.2.26_bk/ blast-2.2.26
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#Get The Weights. We Opted to store the weights in the database at /databases/weights/RFAA_paper_weights.pt To reduce the docker image size. Leaving this here for legacy reasons.
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#RUN wget http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt
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ADD environment.yaml /opt/RoseTTAFold-All-Atom/environment.yaml
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RUN CONDA_OVERRIDE_CUDA="11.8" micromamba install -y -n base -f /opt/RoseTTAFold-All-Atom/environment.yaml && \
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micromamba clean --all --yes
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ENV DB_UR30=/mnt/databases/rfaa/latest/UniRef30_2020_06/UniRef30_2020_06
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ENV DB_BFD=/mnt/databases/rfaa/latest/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
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ENV BLASTMAT=/opt/RoseTTAFold-All-Atom/blast-2.2.26/data/
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ENTRYPOINT ["micromamba", "run", "-n", "base"]
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