[Bioperl-l] Packaging bioperl for Fedora

Alex Lancaster alexl at users.sourceforge.net
Fri Mar 30 03:59:51 EDT 2007


Hello bioperl,

I'm new to the bioperl world, having just started a research position
in which I need to manage a large bioperl-based codebase.  To this
end, I'm working on packaging bioperl as an official Fedora Package
(formerly "Fedora Extras") and I'm currently wading through and
packaging the long laundry list of Perl dependencies (then I'm going
to try and do the same for biopython).  You can see my some of my
progress (including links to the reviews) here:

http://fedoraproject.org/wiki/AlexLancaster

Several issues have arisen during the packaging that I hope the
bioperl list could help clarify:

1) There is one dependent package: perl-SVG-Graph that has
   questionable licensing status that currently prevents it from being
   packaged, see:

   http://bugzilla.redhat.com/233848

   There is no license in any of the documentation or within the .pm
   files, save for the following:

   "COPYRIGHT AND LICENCE

   Copyright (C) 2002-2003 Allen Day <allenday at ucla.edu>,
   Chris To <crsto at ucla.edu>"

   which doesn't really help clarify the situation.  As the original
   upstream authors I have e-mailed both Allen and Chris, but I have
   yet to hear back from them.  Most CPAN modules are usually
   contributed with the implicit "same licensing conditions as Perl",
   but Fedora is strict about stating this explictly.

   If there is anybody on this list who has access to this package
   and/or knows how to contact the upstream authors to clarify the
   license conditions?  Please let me know, or better, if you can
   clarify/fix the license in the CPAN modules itself, then please do!

2) http://www.bioperl.org/wiki/Getting_BioPerl lists 1.4.0 as the
   current "stable" release, but that's getting pretty old, having
   been released back in 2003.  Do you currently recommend people use
   1.4.0 or one of the 1.5.x series?  I'd rather package the more
   recent version even if it's not "officially" stable because I know
   if most bioperl people are using more recent then they'll be calls
   to also package the newest release and doesn't seem sensible to
   spend a lot of time packaging the older release.  If so, is there a
   particular 1.5.x package you recommend, perhaps one which is
   somewhere between totally-stable and bleeding-edge?  (I started on
   1.5.2_102 since it was the latest).

3) Lastly I see that bioperl is now split into bioperl (core),
   bioperl-run, bioperl-db, bioperl-network etc.  Do you recommend
   that each be packaged separately?  For example, I notice that some
   scripts in bioperl (core) actually depends on Perl modules that are
   provided by bioperl-run, which means that they will both be needed
   to installed simultaneously to make rpm happy.
   
Regards,
Alex
--
Alex Lancaster, Ph.D. | Ecology & Evolutionary Biology, University of Arizona



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