perl

[Masha Vecherkovskaya]

It's not that I WANT to use CPAN. It was advised in Circos installation instructions. That is why I asked if I have a chance to mess up everything.

I'm sorry to take your time. My background is medicine/biology (M.D./ PhD). I can follow instructions, when I'm dealing with computer, and I'm not afraid of terminal, but that's about it.
Circos website says:
You do not need to know Perl to run Circos. You do need to be familiar with:

concept of directories and files
navigating directories at the command prompt
creating and deleting directories at the command prompt
concept of absolute and relative paths 
Well I can do that, I have done that:)

And I like learning things.

For example, I don't understand which perl is used when I instmodsh, I guess the one which came with OS? This perl sits in /opt/local/bin/perl?
On the other hand I have a bunch of .pm files that are in opt/local/lib/perl/5.12/5.12.4/different folders

So, does it make a difference where they are? 
I always wanted to ask how does it work, but I guess I'm going to look at it some time this summer, when my research takes a break due to clinic being closed for a month.

Whatever the MacPorts prefix is at this stage I'm not the one to mess around with it.

As I understand, I need to search for all required modules in MacPorts, and install them through MacPorts?

If you think I'm aiming at something I can't achieve, just say so. I won't spend your time and will try to install Circos on my Ubuntu which sits on an old windows laptop. I can mess around there without fear of breaking things, it's not my critical machine, and that system can always be reinstalled.

Thank you

On 28.02.2013, at 15:08, Ryan Schmidt <ryandesign at macports.org> wrote:

> 
> On Feb 28, 2013, at 04:41, Masha Vecherkovskaya wrote:
> 
>> Am I right in feeling (not knowing just feeling), that perl which came with OS X is different from what MacPorts install?
> 
> That might depend on your OS X version. I don't remember what version of perl comes with each version of OS X. But you can see what versions are available in MacPorts and use one you like.
> 
> 
>> If so, will I run into troubles with my ports if I install and use CPAN to install some modules to run a program (http://circos.ca)
> 
> Don't use CPAN to install modules into the MacPorts prefix; find the MacPorts port corresponding to the CPAN module you want and install that instead. Generally, if you want a module Foo::Bar, the port is p5-foo-bar. But you'll want to choose the subport for the version of perl you want, e.g. p5.12-foo-bar. If we don't have a port for the module you want yet, request one, or better yet, create one; the cpan2port script can give you a starting point for that.
> 
> 

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