centos安装samtools

探序基因肿瘤研究院 整理

方法一：git上的代码安装

samtools下载地址：https://github.com/samtools/samtools

还包括有：htslib,bcftools

安装htslib，要安装好他依赖的库，还要yum install automake

运行：autoreconf -i，./configure,

出现错误：

checking whether htscodecs files are present... no
configure: error: htscodecs submodule files not present.

安装samtools:

autoreconf

提示：

configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level

生成了configure

再./configure

checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged

但是make失败

yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel ncurses
-devel libdeflate-devel

输入：autoheader
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level

没安装成功，还是换另一种方法

方法二：源代码包去http://www.htslib.org/download/ 下载，然后编译

./configure,make,make install

安装htslib,samtools,bcftools都行了