1 新建install.sh，内容如下

  1. #!/bin/bash
  2. set -e
  4. if [ ! $1 ] || [ "$1"x == "-h"x ] || [ "$1"x == "--help"x ];then
  5.     echo -e "
  6.     \033[32mone-click install samtools, bcftools and htslib\033[0m
  8. usage: \033[1m`basename $0` version [prefix]\033[0m
  9.        version      the version to install, eg. 1.9
  10.        prefix       the path to install, default: `dirname $(pwd)`/v\$version
  12. contact: suqingdong@novogene.com"
  13.     exit
  14. fi
  16. VERSION=$1
  18. if [ $2 ];then
  19.     INSTALL_DIR=$2
  20. else
  21.     SOURCE_DIR=`pwd`
  22.     INSTALL_DIR=`dirname $SOURCE_DIR`/v${VERSION}
  23. fi
  25. for name in samtools bcftools htslib;do
  26.     if [ ! -f $name-$VERSION.tar.bz2 ];then
  27.         wget -c https://github.com/samtools/$name/releases/download/$VERSION/$name-$VERSION.tar.bz2
  28.     fi
  29. done
  31. tar -xf htslib-${VERSION}.tar.bz2
  32. cd htslib-${VERSION}
  33. ./configure --prefix=${INSTALL_DIR} --disable-lzma
  34. make && make install
  36. cd ..
  37. tar -xf bcftools-${VERSION}.tar.bz2
  38. cd bcftools-${VERSION}
  39. ./configure --prefix=${INSTALL_DIR} --disable-lzma \
  40.     --with-htslib=${INSTALL_DIR}
  41. make && make install
  43. cd ..
  44. tar -xf samtools-${VERSION}.tar.bz2
  45. cd samtools-${VERSION}
  46. ./configure --prefix=${INSTALL_DIR} --disable-lzma \
  47.     --with-htslib=${INSTALL_DIR}
  48. make && make install
  50. echo "
  51. export PATH=${INSTALL_DIR}/bin:\$PATH
  52. export LD_LIBRARY_PATH=${INSTALL_DIR}/lib:\$LD_LIBRARY_PATH
  53. " > ${INSTALL_DIR}/source_this
  54. chmod 755 ${INSTALL_DIR}/source_this
  56. cd ..
  57. rm -rf *-${VERSION}*
  59. echo -e '\033[1;32minstall done !\033[0m'

2 在软件安装目录执行以下命令

  1. sh install.sh 1.9

3 使用时，source一下source_this文件即可