[Bioperl-l] help!

Scott Cain scott at scottcain.net
Tue Feb 7 15:55:25 EST 2012


hi Cassandra,

I don't have an answer for you at the moment.  It seems to me that
using local::lib is a good idea, but I've never found a good tutorial
for using it, so I haven't.  Perhaps someone else on the list can
suggest one.

The other thing I just wanted to mention as the admin that approved
your message--I came very close to deleting it from the queue without
looking at it because it is not unusual for spam messages to have
generic subjects like "help!"  (just for future reference :-)

Scott


On Tue, Feb 7, 2012 at 11:11 AM, Casandra <kasandrah at gmail.com> wrote:
> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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