如何在使用perlbrew时安装最新的BioPerl版本？ [英] How do I install the latest BioPerl version when using perlbrew?

问题描述

我正在使用 perlbrew ，我想安装最新的bioperl版本。我应该使用 cpanm 或 git ？

code> git - 我是否照常安装（AKA git clone ... 然后make和build），还是应该什么特别的？

更新

具体来说，我不确定我是否理解以下来自 BioPerl使用Git手册的专家：

告诉perl哪里可以找到BioPerl
（假设你检出了
$ HOME / src中的代码;将它设置在你的
.bash_profile中。 profile或.cshrc）：

  bash：$ export PERL5LIB =$ HOME / src / bioperl-live：$ PERL5LIB 
 tcsh：$ se $ t $ PERL5LIB$ HOME / src / bioperl-live：$ PERL5LIB
  

为什么这是必要的？

更新2

简单地输出bioperl克隆目录不会影响所有 bp _ ***。pl在正常的 Build 安装之后通常在 / usr / bin / 下找到脚本）。



我也尝试使用 perlbrerw 切换到正确的perl版本后，从克隆的dir构建，但随后它运行cpan shell来安装一些依赖，这些依赖与 perlbrew （而不是 cpanm ）不兼容。 / p>



所以，我的问题仍然存在......

谢谢！

解决方案

最新的 BioPerl 总是会在 GitHub 上，所以git就是你的答案。不管你是否想要流血的边缘是另一回事，但是在遵循BioPerl邮件列表一段时间之后，我感觉开发者更可能说从GitHub安装如果您对BioPerl有任何问题，特别是自 CPAN上的最新版本是从2009年开始的。自那以后，有很多的发展。

不明白你为什么不能继续前进并执行标准的 git clone ... 在使用 perlbrew perl，因为这是 perlbrew 的要点。 ： - ）

更新问题更新：设置 PERL5LIB 因为假设您通过 git 克隆了BioPerl，则无需构建BioPerl;它已经准备好直接使用。假设你还没有将它克隆到 @LIB 目录中，你需要告诉Perl在哪里找到它。无论您是否使用 perlbrew 。

基本上，过程如下所示：

1. 从GitHub克隆BioPerl。


2. 确保您使用 perlbrew -installed Perl。


3. 根据BioPerl指令设置 PERL5LIB 环境变量。 >
   
4. 运行 perl -MBio :: Perl -le'print Bio :: Perl-> VERSION;'确保您使用的是您刚刚签出的BioPerl。

查看源代码，＃4应该打印出1.006900，我认为（或者可能是1.6.9，我永远不能保持Perl版本号直）。

I'm using perlbrew and I would like to install the latest bioperl version. Should I use cpanm or git?

If git - do I just install as usual (AKA git clone ... then make and build), or should I do anything special?

UPDATE

Specifically, I'm not sure I understand the following expert from BioPerl Using Git manual:

Tell perl where to find BioPerl (assuming you checked out the code in $HOME/src; set this in your .bash_profile, .profile, or .cshrc):

bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
tcsh: $ setenv PERL5LIB "$HOME/src/bioperl-live:$PERL5LIB"

Why is this necesary?

UPDATE 2

Simply exporting the bioperl cloned dir does not effect all the bp_***.pl scripts (which are usually found under /usr/bin/ after a normal Build installation).

I also tried to build from the cloned dir after switching to the correct perl version using perlbrerw, but then it runs cpan shell to install some dependencies which does not seem to work well with perlbrew (as opposed to cpanm).

So, my question remains...

Thanks!

解决方案

The latest BioPerl is always going to be on GitHub, so git's your answer there. Whether or not you want bleeding edge is another story, but after following the BioPerl mailing list for some time I get the feeling that the developers are more likely to say "install from GitHub" if you have any problems with BioPerl, especially since the most recent version on CPAN is from 2009. There has been a lot of development since then.

As for installing it, I don't see why you couldn't just go ahead and do the standard git clone ... make/build dance once you're using your perlbrew perl, as that's kind of the point of perlbrew. :-)

Update for question update: The blurb about setting PERL5LIB is there because presumably BioPerl doesn't need to be built once you've cloned it via git; it's ready to use straight out of the box. Assuming you haven't cloned it into a directory in @LIB, you need to tell Perl where to find it. You would have to do this whether or not you are using perlbrew.

Essentially the process goes like this:

1. Clone BioPerl from GitHub.
2. Make sure you're using your perlbrew-installed Perl.
3. Set the PERL5LIB environment variable as per the BioPerl instructions.
4. Run perl -MBio::Perl -le 'print Bio::Perl->VERSION;' to make sure you're using the BioPerl you just checked out.

Looking at the sourcecode, #4 should print out 1.006900, I think (or maybe 1.6.9, I can never keep Perl version numbers straight).

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