[Bioperl-l] Packaging bioperl for Fedora

Lincoln Stein lstein at cshl.edu
Tue Apr 17 13:47:25 EDT 2007


Hi,

I've been updating the WIKI in anticipation of a new GBrowse release and
have added a "stub" for the biopackages.net install. Since I don't use yum
(I've been running Slackware for ages and have recently started working with
Ubuntu) I'm not sure I got the details right. Could someone check?


        http://www.gmod.org/wiki/index.php/GBrowse_RPM_HOWTO

Also, I think some verbiage on how to use yum to install MySQL and Apache
would be great, since it will be consistent with the Ubuntu install page.

Thanks,

Lincoln

On 3/31/07, Brian Osborne <bosborne11 at verizon.net> wrote:
>
> Allen et al.,
>
> What happened to the "GMOD" package or packages? I've had some
> conversations
> in the past few months with you-all suggesting that a GMOD package, or
> packages, would be useful.
>
> Brian O.
>
>
>
>
> On 3/30/07 8:30 PM, "Allen Day" <allenday at gmail.com> wrote:
>
> > Hi Alex,
> >
> > You've aptly noted that there are several classes of packages being
> > discussed here, and that they should not be treated equally.  From my
> > point of view and of specific relevance to the Bioperl community we
> > have at least:
> >
> > 1) "regular" CPAN dependencies and their occassional C/C++/Fortran
> > dependencies.  These should all be in Fedora Extras, as they are of
> > general utility.  Biopackages.net currently hosts about 200 packages
> > (.spec files, specifically) that are like this.  Maybe 80 of these are
> > needed for Bioperl.
> >
> > 2) academic packages, such as BLAT, NCBI Toolkit, CLUSTAL, genscan,
> > etc.  From what I've seen, these typically have strange/custom
> > licenses that may not be valid for some users.  BLAT has a dual
> > licensing scheme for academic and non-academic licensees, for
> > instance.  These packages are not of general utility.  For these two
> > reasons, my stance is that they should not be included in Fedora
> > Extras.
> >
> > 3) Bioperl packages.  Several subsets here.  The Bioperl-run libraries
> > depend directly on type (2) packages, so aren't appropriate to include
> > in Fedora Extras.  Bioperl-live is not really that useful without type
> > (2) packages.  It is also sensible to all of the keep the Bioperl-*
> > packages in the same repository.  For these reasons, my stance is that
> > they should not be included in Fedora Extras.
> >
> > 4) Bioinformatics / Comp. Bio. data sets.  These don't have licensing
> > problems, but they tend to be large.  Usually in the 10E7 - 10E10 byte
> > range.  RPM can not even generate correct metadata for some of them
> > correctly if the files are too large (overflow problems).  Probably
> > not appropriate to put in Fedora Extras because they are too large and
> > not generally useful.
> >
> > 5) Bioinformatics-specific System databases / daemons.  These
> > high-level packages depend on types (2), (3), and (4), and so are not
> > appropriate to put into Fedora Extras.  An example is a BLAT daemon,
> > which relies on the BLAT server, as well as NIB-formatted genome
> > sequence files.
> >
> > That said, there are a lot of type (1) packages in the Biopackages.net
> > repository.  If you're interested in migrating the spec files from our
> > repository to the Fedora project it would save us (the Biopackages.net
> > maintainers) a ton of build and maintenance time, so please feel free
> > to take them, just let us know.  If we can reach some agreement on
> > where the bioinformatics-specific packages should be maintained/built
> > we may be able to work together on these as well.
> >
> > -Allen
> >
> >
> > On 3/30/07, Alex Lancaster <alexl at users.sourceforge.net> wrote:
> >>>>>>> "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)
> >> Extras.
> >>
> >> 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
> >> ones).
> >>
> >> 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
> >> Biopackages.net.
> >>
> >> 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).
> >>
> >> Regards,
> >> Alex
> >>
> >> 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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> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
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>
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724
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