Dockerfile

# Use Ubuntu as base image
FROM ubuntu:22.04

# Avoid prompts from apt
ENV DEBIAN_FRONTEND=noninteractive

# Install system dependencies
RUN apt-get update && apt-get install -y \
    wget \
    git \
    build-essential \
    python3 \
    python3-pip \
    && rm -rf /var/lib/apt/lists/*

# Install Miniconda
ENV CONDA_DIR /opt/conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh

# Add conda to path
ENV PATH $CONDA_DIR/bin:$PATH

# Create conda environment
COPY environment.yml /tmp/environment.yml
RUN conda env create -f /tmp/environment.yml

# Set up working directory
WORKDIR /app

# Copy LSNM files
COPY . /app/

# Make lsnm executable
RUN chmod +x /app/lsnm

# Activate conda environment by default
SHELL ["conda", "run", "-n", "lsnm", "/bin/bash", "-c"]

# Default command
CMD ["/bin/bash"]