[Bioperl-l] Packaging bioperl for Fedora

Allen Day allenday at ucla.edu
Fri Mar 30 14:42:54 EDT 2007

Hi Alex,

The Biopackages.net project is still active, we are regularly adding
packages to it, mostly R packages lately.  Most of the systems we use
are running CentOS at this point, which is why you have not seen
support for FC6 yet.  There is nothing preventing building FC6
packages aside from lack of time to set up the FC6 build farm nodes.

If you're interested in packaging BioPerl or other
bioinformatics-related software, please join the Biopackages project
on SourceForge.  We object to the Fedora Extras FUD tactics used to
discourage people from using 3rd party repositories, and suspect they
may not want to host some of our data packages, such as the >2GB
genome packages.  Biopackages project is likely to partially merge
with RPMForge.  We are already discussing with them how best to do it.


On 3/30/07, Alex Lancaster <alexl at users.sourceforge.net> wrote:
> >>>>> "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

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