Athena/Dockerfile at main · Olympus-R-D/Athena · GitHub

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FROM ubuntu:24.04

# Set environment variables to avoid prompts
ENV DEBIAN_FRONTEND=noninteractive

# Install basic system dependencies
RUN apt-get update && apt-get install -y \
    build-essential \
    cmake \
    git \
    wget \
    unzip \
    libboost-all-dev \
    libssl-dev \
    libffi-dev \
    libyaml-cpp-dev \
    pkg-config \
    && rm -rf /var/lib/apt/lists/*

# Build and install nlohmann/json
WORKDIR /opt
RUN git clone https://github.com/nlohmann/json.git && \
    cd json && mkdir build && cd build && \
    cmake .. && make -j8 && make install && \
    cd /opt && rm -rf json

# Copy and run installation script for bioinformatics tools
ENV CONDA_DIR=/opt/conda
ENV PATH=$CONDA_DIR/bin:$PATH

# Download and install Miniconda (latest)
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh && \
    bash /tmp/miniconda.sh -b -p $CONDA_DIR && \
    rm /tmp/miniconda.sh && \
    conda clean -afy
RUN conda init
RUN bash -c "source ~/.bashrc"

ENV CONDA_ACCEPT_TERMS=true

COPY installation.sh /opt/
RUN chmod +x /opt/installation.sh && bash /opt/installation.sh
RUN ln -s /usr/bin/python3 /usr/bin/python
# Copy ATHENA source code
WORKDIR /athena
COPY ./Athena ./

# Build ATHENA
RUN mkdir -p build && cd build && \
    cmake .. && make -j$(nproc)

# Set PATH to include ATHENA executable
ENV PATH="/opt/quast/:/athena/build:$PATH"

# Create data directory for mounting
RUN mkdir -p /data

# Set working directory to data
WORKDIR /data

# Create a welcome script
RUN echo '#!/bin/bash\n\
echo ""\n\
echo "🧬 Welcome to ATHENA Container! 🧬"\n\
echo "==================================="\n\
echo ""\n\
echo "ATHENA is ready to use. Available commands:"\n\
echo "  athena start     - Run complete pipeline"\n\
echo "  athena fastqc    - Quality control analysis"\n\
echo "  athena trim      - Trimmomatic read trimming"\n\
echo "  athena spades    - Genome assembly"\n\
echo "  athena quast     - Assembly quality assessment"\n\
echo "  athena continue  - Resume from specific step"\n\
echo "  athena help      - Show detailed help"\n\
echo ""\n\
echo "Example usage:"\n\
echo "  athena start -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz -o results/"\n\
echo ""\n\
echo "Your data directory: $(pwd)"\n\
echo "Available files: $(ls -la 2>/dev/null | wc -l) items"\n\
echo ""\n\
exec /bin/bash' > /usr/local/bin/welcome.sh && \
    chmod +x /usr/local/bin/welcome.sh

# Set the entrypoint to welcome script
ENTRYPOINT ["/usr/local/bin/welcome.sh"]