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

[Chris Maloney]

Could you switch master into a feature branch, and put master back to some
last-known-good commit?


On Wed, Jun 25, 2014 at 6:09 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> 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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>
>
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