[Bioperl-l] help!

Joseph Guhlin guhli007 at umn.edu
Tue Feb 7 16:14:05 EST 2012


I wonder if this would work on your system?

http://www.sysarchitects.com/bioperl

Best,
--Joseph Guhlin

On Tue, Feb 7, 2012 at 10:11 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
>
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


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