installation.sh

#!/bin/bash

echo "Starting installation For Athena ..."

if [[ "$OSTYPE" == "linux-gnu"* ]]; then
  if command -v apt-get &> /dev/null; then
      DISTRO="ubuntu"
      echo "Yahoooo"
  else 
    echo "We don't support other distros for now"
    exit 1
  fi
else
  echo "We only support Ubuntu for now"
  exit 1
fi 

command_exits() {
  command -v "$1" >/dev/null 2>&1
}

installation_basic_tools() 
{
  echo "installation basic developement tools ...."
  apt update
  apt install -y cmake default-jre default-jdk
}

installation_bioinformatics_tools()
{
  echo "Installing bioinformatics tools..."
  
  # Core tools
  apt install -y fastqc
  apt install -y trimmomatic  
  apt install -y spades
  
  # Install Python dependencies for bioinformatics tools
  apt install -y python3-pip python3-matplotlib python3-biopython
  
  # Install Perl dependencies for Prokka
  apt install -y libdatetime-perl libxml-simple-perl libdigest-md5-perl bioperl
  
  # Install Bio::Perl from CPAN
  echo "Installing Bio::Perl..."
  cpan -i Bio::Perl
  
  # Install QUAST
  echo "Installing QUAST..."
  cd /opt
  git clone https://github.com/ablab/quast.git
  cd quast
  ./setup.py install_full
  cd /
 
  # Install Prokka
  echo "Installing Prokka..."
  conda create -n prokka_env -c bioconda -c conda-forge prokka && \ conda clean -a -y 
  conda activate prokka_env
  prokka --setupdb
  # Add Prokka to PATH
  echo 'export PATH=$PATH:/opt/prokka/bin' >> /etc/bash.bashrc
  cd /
  
  echo "Bioinformatics tools installation completed!"
}


verify_installtions()
{
  echo "Verifying installations..."
  tools=("java" "cmake" "git" "fastqc" "spades" "trimmomatic" "python3" "quast.py" "prokka")

  for tool in "${tools[@]}"; do 
    if command_exits "$tool"; then 
      echo " ✅ YES : $tool is installed"
    else 
      echo " ❌ NO : $tool is NOT INSTALLED !!!!!!"
    fi 
  done
  
  echo ""
  echo "Testing tool versions:"
  echo "FastQC version: $(fastqc --version 2>/dev/null || echo 'Not found')"
  echo "SPAdes version: $(spades.py --version 2>/dev/null || echo 'Not found')"
  echo "QUAST version: $(quast.py --version 2>/dev/null || echo 'Not found')"
  echo "Prokka version: $(prokka --version 2>/dev/null || echo 'Not found')"
}

main()
{
  echo "Starting installation of Athena env ..."
  installation_basic_tools
  
  echo ""
  installation_bioinformatics_tools
  
  echo ""
  verify_installtions
}

main