circos模块安装

Circos安装

1. 下载软件包

   http://circos.ca/software/download/circos/

2. 解压

   tar -xvzf circos*.tgz

3. 安装模块

#查看依赖项是否安装
cd circos*
./bin/circos -module
#####输出结果
ok       1.26 Carp
missing            Clone
missing            Config::General
ok       3.40 Cwd
ok      2.145 Data::Dumper
ok       2.52 Digest::MD5

[推荐]使用cpanm安装模块

手动安装local::lib模块

• 这里我将所有的perl模块都装到~/perl_lib自定义目录

wget https://cpan.metacpan.org/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz
tar xf local-lib-2.000024.tar.gz
cd local-lib-2.000024
perl Makefile.PL --bootstrap=~/perl_lib
make test && make install

设置环境变量

命令行运行如下命令:

perl -I${HOME}/自定义目录/lib/perl5 -Mlocal::lib=${HOME}/自定义目录

输出内容

PATH="******"; export PATH;
PERL5LIB="******"; export PERL5LIB;
PERL_LOCAL_LIB_ROOT="****${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}"; export PERL_LOCAL_LIB_ROOT;
PERL_MB_OPT="--install_base \"*****""; export PERL_MB_OPT;
PERL_MM_OPT="INSTALL_BASE=****"; export PERL_MM_OPT;

复制输出结果，粘贴到~/.bashrc文件内，

source ~/.bashrc即可

安装cpanm

wget https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7043.tar.gz
tar xf App-cpanminus-1.7043.tar.gz
cd App-cpanminus-1.7043
perl Makefile.PL
make test && make install

使用cpanm

cpanm 模块名
#批量安装缺失模块
circos -module|awk '$1~/missing/{print $2}'|xargs  -I {} cpanm {}

手动安装

从CPAN https://www.cpan.org/ 下载对应的模块源文件

手动安装的配置信息文件 perl_local_config

module_path=/public/home/zpliu/perl_lib/
PREFIX= ${module_path} 
INSTALLSCRIPT= ${module_path} /bin 
INSTALLBIN= ${module_path} /bin 
INSTALLMAN1DIR= ${module_path} /man1 
INSTALLSITELIB= ${module_path} /lib

• PREFIX指定build后路径

#解压源文件
tar -xvzf Clone-0.43.tar.gz
#编译，指定build目标路径
perl Makefile.PL `cat ../perl_local_config `
make 
make test 
make install
#将路径加入环境变量
export PERL5LIB=/public/home/zpliu/perl_lib/lib/:/public/home/zpliu/perl_lib/lib/Module/lib64/perl5/:/public/home/zpliu/perl_lib/lib/Module/share/perl5/

Build.pl类型模块的安装

首先得安装module::build模块

perl build --prefix=/public/home/zpliu/perl_lib/
./Build build
./Build test
./Build install
#添加环境变量
export PERL5LIB=/public/home/zpliu/perl_lib/lib/:/public/home/zpliu/perl_lib/lib/Module/lib64/perl5/:/public/home/zpliu/perl_lib/lib/Module/share/perl5/

perl Build.PL --prefix=/public/home/zpliu/perl_lib/lib/Module/
./Build build
./Build test
./Build install

报错

Can’t locate ExtUtils/PkgConfig.pm

缺失依赖项``ExtUtils::PkgConfig`同样的安装ExtUtils::PkgConfig模块

查看perl中已经安装的模块

instmodsh

• GD模块安装出错，可以使用 libgd 软件替代

  https://comery.github.io/2018/08/15/An-error-when-install-perl-module-GD/

参考

1. perl模块安装 https://www.zhihu.com/question/28532172
2. cpanm https://www.jianshu.com/p/9e90b3524fe2