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Re: Packaging source code for Debian Distributions

Hi again,

since my last mail is 1.5 years ago and one stable Debian release
inbetween.  I wonder whether you might consider to adaptthe license of
blat and the tools around for distribution in Debian.

Kind regards


On Fri, Feb 28, 2014 at 09:46:55AM +0100, Andreas Tille wrote:
> Hi,
> since Jim has given permission to quote him on the list I'll answer here.
> On Thu, Feb 27, 2014 at 12:47:42AM -0800, Jim Kent wrote:
> > Hi Hiram and Ann - I'd like to introduce you to Andreas Tille.  Andreas has
> > been working with me to get blat set up for easy compile and install under
> > Debian.  He is part of a project to get biomedical software, including
> > software with some monetary licensing requirements, more accessible.
> To learn what packages in the field of biology we are maintaining inside
> official Debian you might like to have a look at our tasks list:
>    http://blends.debian.org/med/tasks/bio
>    http://blends.debian.org/med/tasks/bio-dev
> Please note that packages with licensing restrictions according the
> Debian Free Software Guidelines[1] are not part of the Debian
> distribution and also are not included in the metapackages (med-bio and
> med-bio-dev which can be used to install all the software inside Debian
> in one rush).  As long as the license does not permit distribution at
> all it could be packaged and uploaded to non-free and users might be
> able to download from there.
> > He has some interest in doing something similar for the entire UCSC source
> > tree.   Since making our command line software more accessible is one of
> > the aims of our current NHGRI grant,  I think the timing is near perfect
> > for us to work with him on this.
> It would be really cool to work together with you.  We have quite good
> experience by working together with upstream developers.  there is also
> the effort "Mentoring of the Month"
>   https://wiki.debian.org/DebianMed/MoM
> which might help you.
> > Hiram,  could you correspond with Andreas and talk tech and build process
> > with him, and generally get to know him?
> I would really prefer to communicate via the mailing list exclusively
> since we are a team and on one hand we get more input from other team
> members and on the other hand it might be interesting for other people
> learning about your packaging effort soon.
> > One thing we'd need to do that Andreas couldn't,  would be to reorganize
> > the directory structure a bit to make understanding what part is available
> > under what license less of a labyrinth.  They would need to stick the
> > freeware, the UCSC gets $$ for commercial licenses, and the Kent
> > Informatics gets $$ for commercial licenses bits into separate packages,
> >  and I've long felt like we should attempt at least to organize the
> > directory structure to make this more clear.   Something along the line of
> >       kent/src/hg   ->   src/ucsc
> >       kent/src/jkOwnLib -> src/kentInformatics
> >       kent/src/lib   ->    src/freeware
> > Where src/inc and src/utils would end up in freeware as well, as well as
> > hg/autoSql and a few other things that are currently out of place.  The
> > ameme, blat, and waba would end up in kentInformatics as well.
> I perfectly agree that this reorganisation would be a very helpful thing
> to do before we start packaging.  I would also recommend to rework the
> build system (either automake or cmake) to enable
>    a) dynamic & static libraries (since in Debian we usually separate
>       these in different binary packages)
>    b) portability to different architectures (since in Debian the packages
>       are autobuilded for different architectures and this is most easily
>       done if the build system is able to deal with different architectures
>       themselves)
> > Anyway,  Andreas doesn't need to hear all the details of what goes where,
> >  though if has ideas for better high level directory names, it'd be good to
> > hear.
> Finally we need some sensibly craftet versioned release tarballs.  It
> might make sense to create some library releases first and the releasing
> application releases which are using these libraries.
> > Ann, if you could budget some of Hiram's time to work on this it'd be very
> > helpful.   I don't think this is the must be done right away sort of thing,
> >  but once hg38, the new reference genome build,  settles down a bit,  maybe
> > in a 3-6 month time frame,  it would be something Hiram might have time and
> > inclination to spend some serious time on.  If we can keep Andreas'
> > interest we might get some free help with the work too!
> > 
> > Take care,
> >      Jim
> Thanks for your cooperation
>      Andreas.
> [1] https://www.debian.org/social_contract#guidelines
> -- 
> http://fam-tille.de
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