[Bioperl-l] Packaging bioperl for Fedora

Alex Lancaster alexl at users.sourceforge.net
Fri Mar 30 10:25:32 EDT 2007


>>>>> "SC" == Scott Cain  writes:

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

Scott and others,

I did look at biopackages.net, which was helpful, however, I decided
to contribute these as Fedora packages (see below for why), which
means that the build system and infrastructure for the packages are
hosted by the Fedora project itself (rather than by a third-party
repository).

Also the packages on biopackages.net were last updated for Fedora Core
5, which is now 1 year old, so I sort of assumed that the project was
probably on ice at the moment.  Having the packages in Fedora itself
means that the infrastructure is there for new maintainers to pick up
a package if an old maintainer "orphans" it.  Another factor is that
some of the Perl dependencies are required for other (non-Bioperl)
packages in Fedora, (e.g. perl-XML-Writer is used by MythTV) so it
makes sense for these Perl packages to be part of Fedora itself.

Lastly, having Bioperl in Fedora itself means that it can be installed
out-of-the-box without having to enable a new yum repository, which is
why I think it makes sense to have as many bioinformatics packages in
the base distribution and lessens the chance of unexpected
interactions between third-party repositories, see:

http://fedoraproject.org/wiki/Extras/RepositoryMixingProblems

Of course, anybody is welcome to sign up to contribute to Fedora as a
packager, and I'd be happy to either hand off maintainership of (or
co-maintain) these packages to anybody who's interested.  There's a
small amount of hassle signing up and then submitting packages, but
the package peer-review process (as well as a helpful community)
generally helps the quality of packages all round.  For some of the
other packages on biopackages.net, it would be useful to take the spec
files there as a starting point for Fedora packages (e.g maybe for
R-Bioconductor).

Alex
--
Alex Lancaster, Ph.D. | Ecology & Evolutionary Biology, University of Arizona




More information about the Bioperl-l mailing list