Re: Fwd: Prokka Debian package?
Hi Michael,
On Wed, May 20, 2015 at 09:18:17PM +0000, Michael Crusoe wrote:
> On Wed, May 20, 2015 at 3:06 PM Andreas Tille <andreas@an3as.eu> wrote:
>
> > BTW, I have "stolen" your work (stolen in a sense that I took over your
> > changelog entry since I needed to sign it and since beeing in a hurry I
> > completely forgot the option to use -k - if you mind I'll remove the
> > current upload and re-upload with your ID) and uploaded to Debian Med
> > PPA. May be we need to remove from PPA anyway - due to the licensing
> > issues and I simply was to quick (should not work in a hurry :-().
> >
>
> No worries. Out of an abundance of caution I scheduled the package for
> deletion from the PPA (but see below for more on the subject)
Fine. Thanks for cleaning up behind me. ;-)
> Re:
> http://anonscm.debian.org/cgit/debian-med/prokka.git/commit/?id=91b39ca656f979b3c2c704d8756d9e04e54ae5f9
>
> `prokka-tigrfams_to_hmm` & `prokka-make_tarball` are not for end users
> which is why I didn't ship them.
? The code and the description do not match. According to the code you
ship all files in bin/*, right?
BTW, without diving into the code and checking myself I can just quote a
colleague of mine who installed prokka manually that you need to
generate something as root (prokka --setupdb). I have mixed feelings
about this why this needs to be done by root and whether the resulting
files should not rather go to /var/lib/prokka. We should not bloat /usr
by files out of control of dpkg.
> > > However I can still ship the original files plus your prokka-hamap_to_hmm
> > > script and regenerate it at install time.
> > >
> > > Alas the package will not be allowed in Debian main but is allowed in
> > > 'non-free' (or I could split it into a data package in non-free and your
> > > scripts in 'contrib')
> >
> > Something like this. If I understood debian/copyright correctly not all
> > data sets are CC-BY-ND.
>
> 5 of the 8 datasets are CC-BY-ND by my count.
OK and if I understand you correctly all 8 data sets are needed and we
can not go only with the 3 free ones, right?
> > Am I understanding things correctly that the
> > code might serve some purpose with a free subset of data and could be
> > enhanced by other data in non-free + downloaded data?
>
> No, the code is useless without the non-free data :-/
> They take quite a while to generate and the distribution of them is a big
> time saver.
Seems you are refering to README.Debian
Prokka's databases are installed to /usr/share/prokka
HAMAP.hmm is 224M, took 21 hours and 10 minutes, 15M of memory, single threaded?
Shipped HAMAP.hmm is 88M ??
right? Am I understand you correctly that the base data are free and
just the processing of 21hours should be CC-BY-ND? I can not believe
this since this would be insane. Sorry for my naïve question.
> > Has anybody contacted the copyright holders of the data in question?
> >
>
> Upon review of http://www.uniprot.org/help/license I think we may be in the
> clear. CC-BY-NC covers the design and organizational structure of the
> databases in question but facts of nature (the protein sequences) are
> uncopyrightable.
>
> Does that hold up for you?
Definitely. However, I'm not sure whether my personal opinion is
helpful here. I remember I was sending a series of e-mails to authors
of databases shipped with emboss and in the end we were able to clear
out all licenses. No idea in how far this will lead here. In any case
I'm sure that ftpmaster will refuse a package that contains some
CC-BY-ND data (and will probably not dive into a discussion whether
facts of nature are copyrightable or not).
Kind regards
Andreas.
--
http://fam-tille.de
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