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 <[email protected]> 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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