Bioperl的简单快速安装

Bioperl 由于涉及到的包太多,需要超过12000的单独的检测,安装起来比较麻烦,而且很多检测都通不过,对于新手过于繁杂,现在bioperl官网介绍了一种简单快速安装的方法————用第三方工具进行安装,经亲自测试,效果非常好,现简要介绍而下。
1 安装perlbrew(https://perlbrew.pl/)
在终端输入

curl -L https://install.perlbrew.pl | bash

如果系统没有curl命令
对于linux系统

wget -O - https://install.perlbrew.pl | bash

FreeBSD系统

fetch -o- https://install.perlbrew.pl | sh

也可以用cpan安装,在终端输入(注意不需要先打开cpan)

1
2
sudo cpan App::perlbrew
perlbrew init

如果是用cpan安装,perlbrew程序安装在/usr/bin/perlbrew 或者 /usr/local/bin/perlbrew,默认的perlbrew的根目录是~/perl5/perlbrew 。

2 安装cpanm

perlbrew install-cpanm

3 安装Bio::perl

cpanm Bio::Perl

如果找不到cpanm,就输入cpanm的绝对路径

/root/perl5/perlbrew/bin/cpanm Bio::Perl

如果其中报错缺少哪个模块或者哪个模块版本太老,就先安装报错的模块,我的显示是 Test::More 模块版本太老,我就用cpan “install Test::More”就好了。如果正确安装会显示

–> Working on Bio::Perl
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz … OK
Configuring BioPerl-1.007001 … OK
Building and testing BioPerl-1.007001 … OK
Successfully installed BioPerl-1.007001
1 distribution installed

一般在第一步“Working on Bio::Perl”会等一段时间,因为是要下载安装包,只要没有报错,等着就可以了。

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