build_rmats

#!/bin/bash

function show_usage() {
  echo "$0 [--conda] [--no-paired-model] [--no-darts-model]" 1>&2
  echo
  echo '--conda: create a conda environment for Python and R dependencies' 1>&2
  echo '--no-paired-model: do not install dependencies for the paired model' 1>&2
  echo '--no-darts-model: do not install dependencies for the darts model' 1>&2
}

function parse_arguments() {
  local CONDA_FLAG='--conda'
  local NO_PAIRED_FLAG='--no-paired-model'
  local NO_DARTS_FLAG='--no-darts-model'
  USE_CONDA=0
  USE_PAIRED=1
  USE_DARTS=1

  local ARG_ARRAY=( "$@" )
  for ARG in "${ARG_ARRAY[@]}"; do
    if [[ "${ARG}" == "${CONDA_FLAG}" ]]; then
      USE_CONDA=1
    elif [[ "${ARG}" == "${NO_PAIRED_FLAG}" ]]; then
      USE_PAIRED=0
    elif [[ "${ARG}" == "${NO_DARTS_FLAG}" ]]; then
      USE_DARTS=0
    else
      show_usage
      return 1
    fi
  done
}

function set_script_dir() {
  local ORIG_DIR="$(pwd)" || return 1
  local REL_SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" || return 1
  cd "${REL_SCRIPT_DIR}" || return 1
  SCRIPT_DIR="$(pwd)" || return 1
  cd "${ORIG_DIR}" || return 1
}

function create_and_activate_conda_env() {
  local CONDA_ENV_PATH="${SCRIPT_DIR}/conda_envs/rmats"

  conda create --prefix "${CONDA_ENV_PATH}" || return 1
  conda activate "${CONDA_ENV_PATH}" || return 1

  # This lets the build find zlib.h from conda
  export CPATH="${CPATH}:${CONDA_ENV_PATH}/include" || return 1
}

function install_conda_dependencies() {
  # Combine all requirements into a single file so the dependencies can
  # be resolved all at once.
  local ALL_REQUIREMENTS="${SCRIPT_DIR}/conda_requirements.txt"
  local PYTHON_REQUIREMENTS="${SCRIPT_DIR}/python_conda_requirements.txt"
  local PAIRED_REQUIREMENTS="${SCRIPT_DIR}/paired_model_conda_requirements.txt"
  local DARTS_REQUIREMENTS="${SCRIPT_DIR}/darts_model_conda_requirements.txt"
  cp "${PYTHON_REQUIREMENTS}" "${ALL_REQUIREMENTS}" || return 1

  if [[ "${USE_PAIRED}" -eq 1 ]]; then
    cat "${PAIRED_REQUIREMENTS}" >> "${ALL_REQUIREMENTS}" || return 1
  fi
  if [[ "${USE_DARTS}" -eq 1 ]]; then
    cat "${DARTS_REQUIREMENTS}" >> "${ALL_REQUIREMENTS}" || return 1
  fi

  conda install -c conda-forge --file "${ALL_REQUIREMENTS}" || return 1
}

function set_compiler_environment_variables() {
  if [[ -z "${FC}" ]]; then
    export FC="$(which gfortran)" || return 1
  fi
  if [[ -z "${CC}" ]]; then
    export CC="$(which gcc)" || return 1
  fi
  if [[ -z "${CXX}" ]]; then
    export CXX="$(which g++)" || return 1
  fi
}

function build_rmats() {
  GSL_LDFLAGS="$(gsl-config --libs)" || return 1
  GSL_CFLAGS="$(gsl-config --cflags)" || return 1
  export GSL_LDFLAGS || return 1
  export GSL_CFLAGS || return 1
  make || return 1
}

function install_pairadise() {
  if [[ ! -d PAIRADISE ]]; then
    git clone https://github.com/Xinglab/PAIRADISE.git || return 1
  fi

  Rscript install_r_deps.R paired || return 1
}

function install_darts() {
  if [[ ! -d DARTS ]]; then
    git clone https://github.com/Xinglab/DARTS.git || return 1
  fi

  Rscript install_r_deps.R darts || return 1
}

function main() {
  set_script_dir || return 1
  parse_arguments "$@" || return 1
  source "${SCRIPT_DIR}/setup_environment.sh" || return 1

  if [[ "${USE_CONDA}" -eq 1 ]]; then
    create_and_activate_conda_env || return 1
    install_conda_dependencies || return 1
  fi

  set_compiler_environment_variables || return 1
  build_rmats || return 1

  if [[ "${USE_PAIRED}" -eq 1 ]]; then
    install_pairadise || return 1
  fi

  if [[ "${USE_DARTS}" -eq 1 ]]; then
    install_darts || return 1
  fi

  if [[ "${USE_CONDA}" -eq 1 ]]; then
    conda deactivate || return 1
  fi
}

main "$@"