Re: Packaging source code for Debian Distributions
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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