[Bioperl-l] Packaging bioperl for Fedora

Scott Cain cain.cshl at gmail.com
Fri Mar 30 08:48:17 EDT 2007


Hello Alex,

Please take a look at http://biopackages.net/ and talk to Allen Day
and/or Brian O'Connor (that is, Dr. Brian O'Connor :-) as they have
already done most of the work for this: they have FC2 packages for
bioperl and prereqs, they would just need to be updated for more recent
releases of Fedora and bioperl.  Presumably, they would also want to
host the packages at biopackages.net if you do make updated versions.

Scott


On Fri, 2007-03-30 at 00:59 -0700, Alex Lancaster wrote:
> 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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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