[Bioperl-l] help!

Casandra kasandrah at gmail.com
Tue Feb 7 11:11:57 EST 2012


Hi,

I'm trying to install Bioperl but I'm a bit lost. I know I have perl  
installed becaused I have already write some scripts but I'm biologist  
so... not pretty sure about what messages say.

My perl version:
This is perl, v5.8.8 built for darwin-thread-multi-2level
My computer:
Mac OS X Vesion 10.5.8

I was following this preliminary steps:

--------------
PRELIMINARY PREPARATION

    This is optional, but regardless of your subsequent choice of
    installation method, it will help to carry out the following steps.
    They will increase the likelyhood of installation success
    (especially of optional dependencies).

      * Upgrade CPAN:

  >perl -MCPAN -e shell
  cpan>install Bundle::CPAN
  cpan>q				

      * Install/upgrade Module::Build, and make it your preferred
        installer:

  >cpan
  cpan>install Module::Build
  cpan>o conf prefer_installer MB
  cpan>o conf commit
  cpan>q

      * Install the expat library by whatever method is
        appropriate for your system.

      * If your expat library is installed in a non-standard location,
        tell CPAN about it:

  >cpan
  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/ 
non-standard/include"
  cpan>o conf commit
--------------
And I think I did "Upgrade CPAN properly" but when I tried the next  
one it started asking too many things to me, and finally it stopped  
due to "some problems". In text file you can see the whole process.
What did I do wrong?


After solving these preliminary steps, what should I do? What  
exactly .tar or .whatever should I download to install?

I don't see the difference between installing it through "built.PL"  
or  CPAN. And I don't know if I should do this or that "Fink*" stuff  
for MAC.

* I went to Fink webpage and what I expected to see was "hello!  
download Bioperl simply clicking here!" but far from this, what it  
seems is that first I have to download some kinf of Fink-program  
before starting with Bioperl... is it something close to this?

I'm sorry, too many questions... But I really want to learn to use  
Bioperl but I have no people to ask it face to face.

Thank you so much,

Casandra
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