[Bioperl-l] scripts/ and examples/ are merged

[Brian Osborne]

Lincoln,

About a week ago I wrote to this group describing my proposal of merging
these 2 directories and asked for feedback, and I didn't receive any. No
feedback is not a problem but naturally I had to assume that it meant no
objection either, so I went ahead.

Personally I look at these scripts as ways to learn Bioperl, and it's clear
that there's a full spectrum of scripts in scripts/, from minimal to fully
POD-ed and industrial strength. Those little ones could be as useful as the
big ones for purposes of example. But, of course, if there's low-quality
work it's of little utility, I'd suggest just taking them out, I can't see
maintaining a directory of "examples" that we don't think are well-done when
so much care goes into the modules themselves.

Brian O.



-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Lincoln Stein
Sent: Monday, August 26, 2002 11:18 AM
To: Brian Osborne; bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] scripts/ and examples/ are merged

Hi Brian,

I'm not entirely happy about this.  The last I looked there were lots of
scripts in examples that were not industrial strength and really did require
"some assembly."  I will go ahead and flag the ones that I think should be
removed for real (or moved back into examples).

Lincoln

On Monday 26 August 2002 09:11 am, Brian Osborne wrote:
> bioperl-l,
> I'd written earlier that the scripts/ and examples/ directories were
mostly
> indistinguishable. The initial intention was to put POD-ed, "industrial
> strength" scripts in scripts, everything else in examples, but this wasn't
> working out. Now everything's in scripts/, examples/ is gone, and there's
a
> new file called bioscripts.pod which is a POD-ed version of the list of
> scripts that was previously in bioperl.pod, it was invisible there. Now
> scripts/ is loosely organized into directories that roughly mirror the Bio
> directory: "align", "tools", and so on. If you had submitted some scripts
> together in a directory (e.g. "das", "seq", "biblio") then the directory
is
> unchanged, nothing was added to it. A couple of scripts didn't compile, I
> removed them and I'll contact the authors, see if they'd like to try
again.
> And the contributed/ directory is still there, this is for scripts that
> don't use Bioperl.
> All in all this is a very nice collection of scripts and you might want to
> peruse it and look for missing functionality, then contribute any of your
> own to fill in the gaps.
> Brian O.
>
>
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--
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org                                   Cold Spring Harbor, NY
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