Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

2026-03-17 17:57:24 +01:00
commit 6eef3bb748
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+FROM mambaorg/micromamba:1.5.0 AS micromamba
+FROM nvidia/cuda:11.8.0-base-ubuntu22.04
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+ENV MAMBA_USER=root
+ENV MAMBA_USER_ID=0
+ENV MAMBA_USER_GID=0
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+ENV MAMBA_EXE="/bin/micromamba"
+
+# Copy micromamba
+COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
+COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
+COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
+
+RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
+    /usr/local/bin/_dockerfile_setup_root_prefix.sh
+
+SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
+
+# Install system dependencies
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+    wget \
+    git \
+    curl \
+    tar \
+    unzip \
+    build-essential \
+    procps \
+    && rm -rf /var/lib/apt/lists/*
+
+# Activate micromamba for all subsequent commands
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# Install Python first
+RUN micromamba install -y -n base python=3.10 pip -c conda-forge && \
+    micromamba clean --all --yes
+
+# Create working directory
+WORKDIR /opt/RoseTTAFold-All-Atom
+
+# Clone repository
+RUN git clone https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git /opt/RoseTTAFold-All-Atom
+
+# Install SE3Transformer
+RUN pip --no-cache-dir install -e ./rf2aa/SE3Transformer --no-deps
+
+# Install CS-BLAST
+RUN wget -q https://wwwuser.gwdg.de/~compbiol/data/csblast/releases/csblast-2.2.3_linux64.tar.gz -O csblast-2.2.3.tar.gz && \
+    mkdir -p csblast-2.2.3 && \
+    tar xf csblast-2.2.3.tar.gz -C csblast-2.2.3 --strip-components=1 && \
+    rm csblast-2.2.3.tar.gz
+
+# Install BLAST legacy
+RUN wget -q https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz && \
+    mkdir -p blast-2.2.26 && \
+    tar -xf blast-2.2.26-x64-linux.tar.gz -C blast-2.2.26 && \
+    cp -r blast-2.2.26/blast-2.2.26/* blast-2.2.26/ 2>/dev/null || true && \
+    rm blast-2.2.26-x64-linux.tar.gz
+
+# Install conda environment
+COPY environment.yaml /opt/RoseTTAFold-All-Atom/environment.yaml
+RUN CONDA_OVERRIDE_CUDA="11.8" micromamba install -y -n base -f /opt/RoseTTAFold-All-Atom/environment.yaml && \
+    micromamba clean --all --yes
+
+# Set database environment variables
+ENV DB_UR30=/mnt/databases/UniRef30_2020_06/UniRef30_2020_06
+ENV DB_BFD=/mnt/databases/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
+ENV BLASTMAT=/opt/RoseTTAFold-All-Atom/blast-2.2.26/data/
+
+# Create wrapper script
+RUN echo '#!/bin/bash\n\
+cd /opt/RoseTTAFold-All-Atom && python -m rf2aa.run_inference "$@"' > /usr/local/bin/rfaa && \
+    chmod +x /usr/local/bin/rfaa
+
+WORKDIR /workdir
+ENTRYPOINT ["micromamba", "run", "-n", "base"]
+CMD ["rfaa", "--help"]