ELPH+Re: Bio-Linux' Caftools -> experimental Fwd: Processing of caftools_2.0.2-1_amd64.changes
Hello,
On 8/26/18 8:38 PM, Andreas Tille wrote:
> Hi,
>
> On Fri, Aug 24, 2018 at 05:10:07PM +0200, Steffen Möller wrote:
>> This is another Bio-Tools package. I kind of like to have it, but I tend
>> to think this is mostly of historic interest. This does not mean that we
>> should not have it, very much the opposite, it was once instrumental for
>> getting the worm genome together, and many others. Because of the strong
>> educational interest this package should have, the documentation is
>> important which I could not find in the package. Also the man pages are
>> missing. Could you possibly contact upstream about it? And maybe also
>> ask for directions on how the history of Sanger's Human Genome Project
>> can be preserved also on the software side? This could well become a
>> nice paper in its own right, I tend to think. And maybe an dedicated
>> sprint at Sanger on that matter would be a good idea.
> Once there was some discussion here on this list when I was in contact
> with Andrew Page about gubbins packaging (end 2015 / beginning 2016) he
> once was positive about a sprint at Sanger. May be somebody should
> catch up with this and may be even coupling with the yearly MiniDebConf
> in Cambridge is a sensible option (but we should check whether this will
> be held this year).
We should talk back to Sascha about it. There are not too many weekends
left for me this year, others will feel the same. So, let us wait for Tony
to resurface from his vacation and then develop some plan.
>
>> The source tree has some fragments of acedb with it (all developed by
>> the same kind of people) which today is GPLed on
>> https://github.com/richarddurbin/acedb/.
> Hmmm, that's just a code copy of a different version of the acedb
> package. I'd recommend to rather remove it from the caftools package.
Funtionality first. And there is the license incompatibility with the now
GPLed acedb.
>
>> But that is something new. I
>> would guess that there is some interest to also have the CAFTOOLS GPLed.
>> The restrictive nature of their source code is likely because of their
>> competition with Celera at the time and has no meaning today. Could you
>> hence also please ask about a license change?
> That would be really cool. Please record it on our Software Liberation
> page[1].
>
> BTW, what is the reason to upload the package to experimental?
Missing man pages, lack of documentation, and wanted to actively involve
the Bio-Linux folks in the package before it his main.
To unstable I just uploaded ELPH, a sequence motif discovery tool. It
also has
its "redistributionary" roots in Bio-Linux. I added this paragraph to
README.Debian:
"ELPH was previously redistributed as a binary package by the Bio-Linux
distribution. Bio-Linux and Debian-Med jointly work on unifying their
packages. ELPH is hence injected as a regular source package into Debian,
which will render it available also for 64bit Intel and other platforms
like ARM."
I am not exactly sure about why I did that but somehow I felt that it is a
good thing to read about. The vibes it should send out is that we work
out towards
platform independence and large user bases. If you have other ideas about
how to word something like that, please go ahead.
Best,
Steffen
>
> [1] https://wiki.debian.org/DebianMed/SoftwareLiberation
>
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