Re: Fate of Bio::Perl newbie module?
Hi,
On Wed, Nov 27, 2019 at 12:08:08PM +0000, Carnë Draug wrote:
> On Wed, 27 Nov 2019 at 10:52, Andreas Tille <andreas@an3as.eu> wrote:
> > > The Bio::Perl module is on the Bio-Procedural repository [1]. No one
> > > has picked up its maintenance and remains unreleased so you won't find
> > > it on CPAN.
> >
> > Would you volunteer to take over this one?
>
> I'm sorry but I can't.
>
> > If not could you give some
> > short intro what is needed to do to get that module back on CPAN?
>
> Sure. Someone will need to show interest on take over maintenance of
> it. To do so, I would open an issue on the repo [2] saying that I was
> interested. This person will need a PAUSE account [3]. The admin of
> the BIOPERLML on PAUSE (that's cjfields) will need to give permissions
> to that person.
>
> The distribution is already setup to be released with bioperl's dzil
> plugin bundle [4]. The instructions are there.
>
> I think a maintainer should at least address issues #1 [5] and #2 [6]
> before making the release.
Thanks for the introduction. For me as a non-Perl programmer that's way
to complex since even if I make it through the procedure I could not
take over any maintenance of a Perl module.
> Also, beware of the following optional dependencies which are not part
> of the core BioPerl distribution (not sure if already packaged in
> Debian):
>
> * Bio::DB::EMBL
> * Bio::DB::GenBank
> * Bio::DB::GenPept
> * Bio::DB::RefSeq
> * Bio::Tools::Run::RemoteBlast
>
> As well as these also optional dependencies which are also not on CPAN
> yet:
>
> * Bio::DB::RefSeq [7]
> * Bio::DB::SwissProt [8]
Adding some other lib#AvailableOnCPAN#-perl package seems to be a
feasible thing to do, thought. Also if there is some maintained
upstream source outside CPAN should be fine.
So the question is:
Do we have some Perl programmer in the Debian Med team who is
willing to follow the procedure described above?
If the answer is no, what do we do to salvage packages like prokka and
possibly others since it seems the old bioperl is broken appart that
strongly that other packages relying on it will be broken as well. Is
the answer that we revert the version bump any rely on the old
monolithic bioperl or should we talk about the problem with upstreams of
prokka (and may be others) to change their code to only use maintained
bioperl modules?
Kind regards
Andreas.
> [2] https://github.com/bioperl/Bio-Procedural/issues/
> [3] https://pause.perl.org/pause/query
> [4] https://metacpan.org/pod/Dist::Zilla::PluginBundle::BioPerl#Pushing-releases
> [5] https://github.com/bioperl/Bio-Procedural/issues/1
> [6] https://github.com/bioperl/Bio-Procedural/issues/2
> [7] https://github.com/bioperl/Bio-DB-RefSeq
> [8] https://github.com/bioperl/Bio-DB-SwissProt
--
http://fam-tille.de
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