content: # Use the same base image as the original (you may need to adjust this)
  FROM ubuntu:20.04
  
  # install app dependencies
  RUN apt-get update && apt-get install -y \
          hmmer \
          infernal infernal-doc \
          git \
          lua5.3 \
          curl \
          wget \
          && rm -rf /var/lib/apt/lists/*
  
  # Install Julia
  RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.10/julia-1.10.5-linux-x86_64.tar.gz \
      && tar -xzf julia-1.10.5-linux-x86_64.tar.gz \
      && mv julia-1.10.5 /opt/julia-1.10.5 \
      && rm julia-1.10.5-linux-x86_64.tar.gz
  
  # Add Julia to PATH
  ENV PATH="/opt/julia-1.10.5/bin:$PATH"
  # Set Julia load path to include Emma
  ENV JULIA_LOAD_PATH="/opt/Emma:/opt/Emma/src:$JULIA_LOAD_PATH"
  # Make sure the Julia environment is activated by default
  ENV JULIA_PROJECT="/opt/Emma"
  
  # Copy Emma source code
  RUN git clone https://github.com/ian-small/Emma /opt/Emma
          
  # Set up Julia environment for Emma
  WORKDIR /opt/Emma
  
  # Install Emma dependencies and precompile
  RUN julia --project=. -e 'using Pkg; Pkg.instantiate()'
  
  # Add additional required packages to the Emma project
  RUN julia --project=. -e 'using Pkg; \
          Pkg.add("FASTX"); \
          Pkg.add("BioSequences")'
  
  # Precompile Julia packages and create cache files
  RUN julia --project=. -e 'using Pkg; Pkg.precompile()'
  
  # Load Emma to create all necessary cache files
  RUN julia --project=. -e 'using Emma; println("Emma loaded successfully")'
  
  # Copy extract_proteins script
  COPY extract_proteins.jl /opt/.
  RUN chmod +x /opt/*.jl
  
  # Set working directory back to root
  WORKDIR /
  
  # Final test
  RUN julia -e 'using Emma; println("Emma available in global environment")'
  
  
  
  
  