Dockerfile

# Use an official Miniconda image as a base
FROM continuumio/miniconda3:latest

# Set working directory
WORKDIR /app

# Install system dependencies (HMMER, BLAST, and others)
RUN apt-get update && apt-get install -y \
    build-essential \
    procps \
    && rm -rf /var/lib/apt/lists/*

# Copy the environment file
COPY RREfinder.yml .

# Create the Conda environment
RUN conda env create -f RREfinder.yml

# Make RUN commands use the new environment
SHELL ["conda", "run", "-n", "RREFinder", "/bin/bash", "-c"]

# Install Flask and other Python dependencies not in the yml
COPY requirements.txt .
RUN pip install -r requirements.txt

# Copy the rest of the application
COPY . .

# Setup exploratory mode (runs the script to set paths)
# Note: This might require some interaction or env vars, 
# so we ensure it runs non-interactively if possible.
RUN python setup_RRE_exploratory.py

# Download the databases (This might take some time)
RUN python download_RRE_databases.py

# Expose the Flask port
EXPOSE 5000

# Set environment variables for Flask
ENV FLASK_APP=app.py
ENV FLASK_RUN_HOST=0.0.0.0

# Start the application using conda run to ensure the environment is active
CMD ["conda", "run", "--no-capture-output", "-n", "RREFinder", "python", "app.py"]