install.sh

#!/bin/bash

# Default value for args
finalize_only=false
data_repo_loc=${HOME}

# Help function
function show_help {
  echo "Usage: script.sh [--finalize_only] --data_repo_loc <data_repo_loc>"
  echo "Options:"
  echo "  --finalize_only          Do not install AA or AC. Only finalize data repo and mosek license location"
  echo "  --data_repo_loc <path>   Custom set data repository location (defaults to creating a directory in \$HOME}"
}

# Parse command line options
while [[ $# -gt 0 ]]; do
  case "$1" in
    --finalize_only)
      finalize_only=true
      shift
      ;;
    --data_repo_loc)
      if [[ -n $2 ]]; then
        data_repo_loc=$2
        shift 2
      else
        echo "Error: Missing argument for --data_repo_loc" >&2
        show_help
        exit 1
      fi
      ;;
    -h|--help)
      show_help
      exit 0
      ;;
    *)
      echo "Error: Unknown option: $1" >&2
      show_help
      exit 1
      ;;
  esac
done

if ! command -v samtools &> /dev/null; then
    echo "error! samtools is not installed or not on the system path!"
    exit 1
else
    echo "samtools is installed and on the system path"
fi

if ! command -v bwa &> /dev/null; then
    echo "error! bwa is not installed or not on the system path!"
    exit 1
else
    echo "bwa is installed and on the system path"
fi

# install the src code and set bash vars if needed
if ! ${finalize_only}; then
  # pull source code for AA
  TARGET="AmpliconArchitect"
  if [ -d "TARGET" ]; then
    echo "Directory '${PWD}/${TARGET}' already exists."
  else
    git clone https://github.com/jluebeck/$TARGET.git
  fi

  # pull source code for AC
  TARGET="AmpliconClassifier"
  if [ -d "TARGET" ]; then
    echo "Directory '${PWD}/${TARGET}' already exists."
  else
    git clone https://github.com/jluebeck/$TARGET.git
  fi

  # install deps
  python3 -m pip install cnvkit Flask future intervaltree "matplotlib>=3.5.1" mosek numpy pysam scipy


  if [ -z "$AA_SRC" ]; then
    echo export AA_SRC=$PWD/AmpliconArchitect/src/ >> ~/.bashrc
    export AA_SRC=$PWD/AmpliconArchitect/src/
  else
    echo "WARNING: AA_SRC bash variable is already set! If you do not want to continue using your old AA installation, remove AA_SRC from your ~/.bashrc file and run the installer again!" >&2
    echo "Proceeding with AA `python3 $AA_SRC/AmpliconArchitect.py -v`"
  fi

  if [ -z "$AC_SRC" ]; then
    echo export AC_SRC=$PWD/AmpliconClassifier >> ~/.bashrc
    export AC_SRC=$PWD/AmpliconClassifier
  else
    echo "WARNING: AC_SRC bash variable is already set! If you do not want to continue using your old AC installation, remove AC_SRC from your ~/.bashrc file and run the installer again!" >&2
    echo "Proceeding with AC `python3 $AC_SRC/amplicon_classifier.py -v`"
  fi

fi

if [ -z "$AA_DATA_REPO" ]; then
  data_repo_path=${data_repo_loc}/data_repo
  echo "Creating new data repo in ${data_repo_path}"
  # make a directory for the AA data repo and create an empty file for coverage summaries to be stored when running AA
  mkdir -p ${data_repo_path}
  touch ${data_repo_path}/coverage.stats
  chmod a+rw ${data_repo_path}/coverage.stats
  echo export AA_DATA_REPO=${data_repo_path} >> ~/.bashrc
  export AA_DATA_REPO=${data_repo_path}

else
  echo "AA_DATA_REPO variable already set to ${AA_DATA_REPO}. To change this remove AA_DATA_REPO from your ~/.bashrc file and run the installer again!" >&2

fi

# this is where the license will go
mkdir -p ${HOME}/mosek/

if ! test -f "${HOME}/mosek/mosek.lic" && ! test -f "${MOSEKLM_LICENSE_FILE}/mosek.lic"; then
  echo "Now obtain license file mosek.lic (https://www.mosek.com/products/academic-licenses/). Move the file to ${HOME}/mosek after downloading. The license is free for academic use."
else
  echo "Mosek license already in place"

fi

echo "Reloading ~/.bashrc"
source ${HOME}/.bashrc

if ! "${finalize_only}"; then
  echo "Module versions are..."
  echo "AmpliconSuite-pipeline: `python3 AmpliconSuite-pipeline.py -v`"
  echo "AA: `python3 $AA_SRC/AmpliconArchitect.py -v`"
  echo "AC: `python3 $AC_SRC/amplicon_classifier.py -v`"
fi

echo "Finished configuring"