Bioperl-guts: 'releaseable system', Makefile.PL issues and documentation
Steve A. Chervitz
Wed, 23 Sep 1998 17:19:25 -0700 (PDT)
> Chris - if we don't have this in place edit of
> the # business then does the makefile make fine (thta
> is not my experience btw). I was messing around with it
> today with no luck.
The inplace editing shouldn't make a difference. It's likely a
directory location issue. I know that the Makefile process is picky
about where modules are located. I'll take a look at it later.
> Perhaps a more robust solution is to split off the poorly
> used IO into another package (? SeqIO.pm) The IO issues are
> almost like factory issues anyway, not methods, so it is
> not so stupid (but then... I guess reading some foramts
> should be in the Seq.pm object). Decisions, decisions,
> decisions... stevec: do you autosplit modules regularly?
> What are we doing wrong at the moment?
I like the idea of having a separate SeqIO.pm module for the less
common formats. You may have noticed in the current Seq.pm I'm not
autoloading the simple fasta and raw IO methods since they are short,
simple, and commonly used.
> RE; documentation -- I like the outline. think there needs
> to be something that gives a real basic view of bioperl,
> in particular for people who are expecting bioperl to be much
> more a collection of scripts than a collection of modules.
> Perhaps in the DOC-INDEX.pod (? maybe this could be bioperl.pod...
> then perldoc bioperl would get you it.)
This would be a good idea. However, I'd recommend putting it in the
README file. I would also recommend placing the install instructions
in the README file and *not* having a separate INSTALL file. This is
standard practice and simplifies the doc structure.
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