方法一:使用CPAN安装
1。使用CPAN模块下的Bundle::BioPerl安装:
>perl -MCPAN -e "install Bundle::BioPerl"
2。如果不成功,执行以下命令
> perl -MCPAN -e shell Then find the name of the Bioperl version you want: cpan>d /bioperl/ CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata Database was generated on Mon, 20 Nov 2006 05:24:36 GMT Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz选择一个安装
cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz或是用 force强制安装。这样不会报错。推荐。 If you decide that the failed tests will not affect how you intend to use Bioperl and you'd like to install anyway do:
cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz 接下来就是会出现一些选择。基本上我都是选Y[yes],或A[all]。附:执行perl -MCPAN -e shell出错,提示如下: [root@fc9 ~]# perl -MCPAN -e shell Can't locate CPAN.pm in @INC (@INC contains: /usr/lib/perl5/5.10.0/i386-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl .). BEGIN failed--compilation aborted
方法二:
下载BioPerl,目前的最新版本是BioPerl-1.6.0
下载Build.PL,右键另存为。
接下来就是解压BioPerl,然后运行Build.PL安装。
>tar xvfz BioPerl-1.6.0.tar.gz>cd BioPerl-1.6.0
>perl Build.PL
>make >make test If you decide that the failed tests will not affect how you intend to use Bioperl and you'd like to install anyway do: >make install 成功进入CPAN的shell模式
[root@fc9 CPAN-1.9205]# perl -MCPAN -e shell 很多 linux 的发行版已经有对应的安装包可以直接安装,如我使用的 debian 目前就提供 Bioperl 1.4 的deb包可以直接安装,使用apt-get install 一行命令直接搞定,无比方便。linux 下装好的 Bioperl 模块一般在如下地址:
/usr/local/share/perl5.X.X/lib/Bio/此外,如果你想使用最最新的开发版本,也就是 Bioperl 开发者们目前使用并不断在更新的版本,你可以使用open-bio.org 的匿名 CVS 服务器。
在连结到 internet 的情况下,使用如下命令:
cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login输入密码: cvs
然后 check out 你想要的:
cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl checkout bioperl-live在linux下的安装参照
# $Id: INSTALL,v 1.38 2005/02/22 23:39:58 bosborne Exp $ o BIOPERL INSTALLATION o SYSTEM REQUIREMENTS o OPTIONAL o ADDITIONAL INSTALLATION INFORMATION o THE BIOPERL BUNDLE o INSTALLING BIOPERL THE EASY WAY USING CPAN o INSTALLING BIOPERL THE EASY WAY USING 'make' o WHERE ARE THE MAN PAGES? o EXTERNAL PROGRAMS o INSTALLING BIOPERL SCRIPTS o INSTALLING BIOPERL IN A PERSONAL MODULE AREA o INSTALLING BIOPERL MODULES THE HARD WAY o USING MODULES NOT INSTALLED IN THE STANDARD LOCATION o THE TEST SYSTEM o BUILDING THE OPTIONAL bioperl-ext PACKAGE o DEPENDENCIES AND Bundle::BioPerl o BIOPERL INSTALLATION Bioperl has been installed on many forms of Unix, Win9X/NT/2000/XP, and on Mac OS (