[Bioperl-l] Build.PL? Can't I just use bioperl-live from github? (rosalind.info looks cool)

[Fields, Christopher J]

Hi Jay.

We’ve been working on splitting out BioPerl modules, including Bio::Root, into separate distributions.  So yes you are catching us in the middle of a (very long and drawn out) transition.

If you want the old version, it is on the v1.6.x branch, which still includes the Root modules.

chris

On Jun 25, 2014, at 4:07 PM, Jay Hannah <jay at jays.net> wrote:

> Hi BioPerl! 
> 
> I've been gone a long time. I'm sitting here at YAPC, someone mentioned http://rosalind.info/ Cool! Hey, I'll do some of these with BioPerl, just for fun! Woot! 
> 
> I'm surprised, sad, that I'm having a hard time using BioPerl on my laptop. I just wanted to use Bio::Seq:
> 
> BioPerl-Rosalind git:(master) $ perl dna.pl
> Can't locate Bio/Seq.pm in @INC ...
> 
> Oh, right. No problem, I'll just add BioPerl to my PERL5LIB:
> 
> BioPerl-Rosalind git:(master) $ export PERL5LIB=~/src/bioperl-live
> BioPerl-Rosalind git:(master) $ perl dna.pl
> Base class package "Bio::Root::Root" is empty. ...
> 
> Uhh... what? Do I have to install BioPerl? That's a bummer, well, OK, I guess if I HAVE TO install, I will:
> 
> bioperl-live git:(master) $ perl Build.PL
> Can't locate Bio/Root/Build.pm in @INC ...
> bioperl-live git:(master) $ find ./ -name "Build.pm"
> bioperl-live git:(master) $ 
> 
> Wait... what? Years ago I used BioPerl from github for years... Have I completely forgotten how everything works?
> 
> If I "fix" it would I be breaking it? 
> 
> Chris: Are you in the middle of some transition?
> 
> -------------------------------------------------------------
> bioperl-live git:(master) $ git log Build.PL
> commit a747f2054b2a85526eda382baf498a945a9817d2
> Author: Chris Fields <cjfields at bioperl.org>
> Date:   Tue May 27 10:33:21 2014 -0500
> 
>    Revert "Move Build.pm out of Root into an install-specific directory; this will"
> 
>    This reverts commit 268b046514e9e4cd7b67f346c524ff04b8a3aa5e.
> 
> commit 268b046514e9e4cd7b67f346c524ff04b8a3aa5e
> Author: Chris Fields <cjfields at bioperl.org>
> Date:   Tue May 27 00:54:25 2014 -0500
> 
>    Move Build.pm out of Root into an install-specific directory; this will
>    eventually lead up to factoring as much out of it as possible (and maybe
>    deprecating it altogether)
> -------------------------------------------------------------
> 
> ...
> 
> To my shock and horror (j/k lolz), I've been coding Perl for almost 20 years, yet BioPython Just Works:
> 
> biopython git:(master) $ python setup.py build
> biopython git:(master) $ python setup.py test
> 
> Why is Python easier to use than Perl, when I'm a Perl guy and don't know squat about Python?
> 
> ...  Can I help fix things?
> 
> Thanks,
> 
> j
> http://www.bioperl.org/wiki/Jay_Hannah
> 
> 
> 
> 
> 
> 
> 
> 
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