[Bioperl-l] Packaging bioperl for Fedora

Brian O'Connor boconnor at ucla.edu
Wed Apr 18 15:00:32 EDT 2007


Hey Lincoln,

This looks good but the configuration step is about to change for 
Biopackages.  I'm writing config RPMs today so the end user can just 
install the config RPM for their distro and they don't have to manually 
change the yum.conf file.  It will also install the biopackages gpg key 
too so we can support signed packages.  I'll update the wiki when these 
config RPMs are available.

--Brian

Lincoln Stein wrote:

> Hi,
>
> I've been updating the WIKI in anticipation of a new GBrowse release 
> and have added a "stub" for the biopackages.net 
> <http://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 
> <mailto: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
>     <mailto: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 <http://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 <http://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 <http://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
>     <mailto:alexl at users.sourceforge.net>> wrote:
>     >>>>>>> "AD" == Allen Day  writes:
>     >>
>     >> AD> Hi Alex, The Biopackages.net <http://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
>     <http://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
>     <http://Biopackages.net>.  Also packages which can't be
>     >> packaged by Fedora for legal reasons like Clustal could/should
>     go in
>     >> Biopackages.net <http://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
>     <http://Biopackages.net> is alive and well and
>     >> I welcome a discussion on how upstream Fedora can usefully interact
>     >> with Biopackages.net <http://Biopackages.net> (I guess perhaps
>     on the Biopackages.net <http://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
>     >>
>     >>
>     >>
>     >> _______________________________________________
>     >> Bioperl-l mailing list
>     >> Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
>     >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>     >>
>     > _______________________________________________
>     > Bioperl-l mailing list
>     > Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
>     > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>     _______________________________________________
>     Bioperl-l mailing list
>     Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
>     http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu <mailto:michelse at cshl.edu> 




More information about the Bioperl-l mailing list