[Bioperl-l] Packaging bioperl for Fedora

Alex Lancaster alexl at users.sourceforge.net
Fri Mar 30 19:52:08 EDT 2007

>>>>> "AD" == Allen Day  writes:

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

Hi Allen and other,

Great news to hear that Biopackages.net is still active!  I would like
to help out if possible.  I don't believe in "FUD" either... ;)

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

The packages that I created which are currently available in Fedora
Packages are Perl dependencies which, as I said are useful for
packages outside the bioinformatics purview.  I do have a (base)
bioperl package in review, but it is not yet released.

As for third-party repos, I don't object to them at all, and for some
kinds of projects they are indeed appropriate. (e.g. for non-free
stuff like Livna or Freshrpms).  However I do have practical concerns
about repository mixing, but I think that it does need to be handled
carefully but that co-operation between Fedora and third-party repos
can make it work.

For example, one practical concern is that as of the
soon-to-be-released Fedora 7, Core+Extras will be merged, so there
will be no distinction at the repository-level between formerly Extras
packages and formerly Core packages (as of now there are only "Fedora
Packages"), which means that it will not be possible for third-party
repos to limit their dependencies to just those in a former base set
(i.e. excluding Extras).

I agree that a few years ago (circa 2003-2004) there was concern about
the way some third party repositories were treated somewhat badly by
the (then) Fedora Extras (with some people going so far as to say that
third-party repos were bad in principle and should always be ignored
which I disagree with too).  But it seems to me that culture has
shifted since, with some notable packagers such as Matthias Saou (of
Freshrpms) and Axel Thimm (of Atrpms) now contributing packages to
Fedora itself.  The process of contributing has also become much
simpler and reviews are conducted speedily and efficiently, I had
packages in the repository in a matter of a few days from initial
submission.  Freshrpms itself now enables and depends on the (old)

The real question for me, then is what packages it makes sense to go
in Fedora, and what packages go in third party repositories.  It seems
to me that in the case of Perl packages which could be dependencies
for other packages not specific to the third-party repo in question,
it makes sense for them to go into Fedora itself, so I think I will
continue to package them.  This lessens the load on the third-party
repo, while making them available for all other third-party repos.
(This is approach that Freshrpms seems to be taking, Matthias has
contributed most packages back to Fedora now other than the non-free

At the other end of the spectrum are packages like you mention, genome
packages, which may be of concern because of their size and/or highly
specialised nature, and, as you say, may make sense to go in a
third-party repo like Biopackages.net.  Also packages which can't be
packaged by Fedora for legal reasons like Clustal could/should go in

In the middle are packages like bioperl itself which are potentially
useful to perhaps a wider group of people than the genome packages but
may not necessarily be dependencies for other packages.  I lean
towards making them part of Fedora so that they will be available of
out the box on the planned "Everything" DVD ISO, but I welcome a
discussion on this.

As I said, I'm glad to hear that Biopackages.net is alive and well and
I welcome a discussion on how upstream Fedora can usefully interact
with Biopackages.net (I guess perhaps on the Biopackages.net list).


PS.  As the upstream author If you could clarify the license on
perl-SVG-Graph, on CPAN (or on the mailing list) that would be great.
Alex Lancaster, Ph.D. | Ecology & Evolutionary Biology, University of Arizona

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