#!/bin/bash

set -e

source "$(
  cd "$(dirname "$0")" || exit 1
  pwd
)/../common.sh"

# 安装编译前必要应用
function install_development() {
  sudo yum install -y wget tar libatomic environment-modules zlib-devel bzip2 bzip2-devel ncurses-libs ncurses-devel xz-devel
  source /etc/profile
}

# 下载samtools
function download_samtools() {
  echo "# samtools正在下载"
  wget -t 40 -c -P "$1" https://udomain.dl.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2
  if [[ $? -eq 0 ]]; then
    echo -e "\033[1;32;1m# samtools已经下载成功\033[0m"
  else
    echo -e "\033[31m# samtools下载失败,请重新执行脚本\033[0m"
    exit 1
  fi
}

# 安装samtools
function install_samtools() {
  echo "# samtools正在安装"
  tar xf "$1"/samtools-0.1.19.tar.bz2 -C "$1" && rm -rf "$1"/samtools-0.1.19.tar.bz2
  cd "$1"/samtools-0.1.19
  sed -i -e 's/gcc/clang/g' Makefile
  make
  mkdir -p "$2"/samtools-0.1.19 && cp -r "$1"/samtools-0.1.19/* "$2"/samtools-0.1.19/
  echo -e "\033[1;32;1m# samtools已经安装完毕\033[0m"
}

# 创建samtools的modulefiles
function write_samtools_module() {
  cat>"$1/samtools-0.1.19/samtools_modulefiles"<<EOF
#%Module1.0
conflict samtools
variable modfile [file normalize [info script]]
proc getModulefileDir {} {
  variable modfile
  set modfile_path [file dirname \$modfile]
  return \$modfile_path
}
set pwd [getModulefileDir]
set SAMTOOLS \$pwd
setenv SAMTOOLS \$SAMTOOLS
prepend-path PATH \$SAMTOOLS/bin
EOF
}

function main() {
  print_current_running_script_info "samtools-0.1.19.sh"
  # 校验安装路径与构建路径是否一致
  is_equal_build_install_path "$1" "$2"
  # 安装编译前应用
  install_development
  # 下载
  download_samtools "$1"
  # 安装
  install_samtools "$1" "$2"
  # 写入modulefiles
  write_samtools_module "$2"
  # 删除构建路径
  rm -rf "$1"/samtools-0.1.19
}

main "$@"