install

#!/bin/bash

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 install_conda() {
  conda create --prefix "${CONDA_ENV_PREFIX}" || return 1
  conda activate "${CONDA_ENV_PREFIX}" || return 1

  conda install --override-channels -c conda-forge -c bioconda --file \
        "${SCRIPT_DIR}/conda_requirements.txt" || return 1

  # The CFLAGS and CPPFLAGS environment variables will be used when compiling.
  # The compile commands can be seen with:
  #   python -m pip install --verbose .
  python -m pip install . || return 1

  conda deactivate || return 1
}

function write_conda_wrapper_config() {
  local CONFIG_PATH="${SCRIPT_DIR}/snakemake_config.yaml"
  echo "conda_wrapper: '${SCRIPT_DIR}/conda_wrapper'" \
       >> "${CONFIG_PATH}" || return 1
}

function main() {
  set_script_dir || return 1
  source "${SCRIPT_DIR}/set_env_vars.sh" || return 1
  install_conda || return 1
  write_conda_wrapper_config || return 1
}

main "$@"