Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Ben,
would you volunteer to contact the authors about this?
Thanks a lot in advance
Andreas.
On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote:
> I was referring to the flappy license, that is mozilla like
> maybe they are willing to change to MPL-2.0 that is GPL compatible
> if that research only is a problem, but I think (guess) there are
> enough escapes in the license.
>
> I still think there should be a confirmation
> that guppy will not be available with a free software
> license. Because I think it is developed with
> contributions from the community.
>
> Otherwise it is indeed non-free.
>
> Based on the flappy license, should asked to release guppy with MPL-2.0?
>
> Someone mentioned chiron, maybe that is the only good alternative at
> this moment?
> (the Basecalling-comparison contains some additional advice on chiron
> settings)
>
> On 28-04-20 10:11, Andreas Tille wrote:
> > Hi Michael,
> >
> > thanks a lot for the links. Any volunteer to start some discussion?
> > As I said: If we do not try nothing will change. People with no
> > technical skills could contribute by doing so to take some workload
> > from packagers.
> >
> > I'll offer a $DRINK at next Debian Med sprint for every attempt to
> > change a license. ;-)
> >
> > Kind regards
> >
> > Andreas.
> >
> > On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:
> >> The guppy binary license is
> >> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
> >> No source code is provided. No competitors of the company may use the
> >> software. Must be for "research use only".
> >>
> >> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
> >> license some of their "source available" software
> >> Only permits "research purposes", violating DFSG guideline #6 "No
> >> Discrimination Against Fields of Endeavor"
> >>
> >> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
> >> Public License and is DFSG compatible
> >>
> >> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <benattris@gezapig.nl> wrote:
> >>
> >>> Sorry to pop in.
> >>> I think this license should be reviewed,
> >>> unless sure it is not a free license.
> >>> To me it looks like a free software license.
> >>> Although not understand most.
> >>>
> >>> What is making this license non-free?
> >>>
> >>> On 27-04-20 17:06, Jun Aruga wrote:
> >>>> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <tille@debian.org> wrote:
> >>>>> Hi again,
> >>>>>
> >>>>> this brings up again my point: We *really*, *really* should take the
> >>>>> chance right now to ask upstreams for free licensing. The time is good.
> >>>>> We just need somebody who is really doing this.
> >>>> For us, the free licensing is good. But for the company nanopore
> >>>> technologies it is their core competency.
> >>>> I am not sure we can make it happen, but it might be worth trying to ask.
> >>>>
> >>>>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> >>>>>> Extracting the linked deb, one finds a binary and a very restrictive
> >>>>>> license. I do not believe that guppy source code is available nor it is
> >>>>>> likely to become available any time soon.
> >>>>>>
> >>>>>> While some of their other basecallers have source code available, I
> >>> would
> >>>>>> not call the license OSS:
> >>>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >>>> I found guppy client software that might be an alternative to use
> >>>> guppy's function.
> >>>> https://github.com/nanoporetech/pyguppyclient
> >>>>
> >>>> As Michael mentioned, checking other basecallers for nanopore, then
> >>>> communicating the nf-core/nanoseq project using the alternative base
> >>>> caller optionally.
> >>>>
> >>>> I found an interesting document about the basecallers.
> >>>> https://github.com/rrwick/Basecalling-comparison
> >>>>
> >>>> Performance of neural network basecalling tools for Oxford Nanopore
> >>> sequencing
> >>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> >>>>> In this study, we tested four basecalling programs developed by ONT –
> >>> Albacore, Guppy, Scrappie and Flappie
> >>>>> ...
> >>>>> We also tested Chiron (https://github.com/haotianteng/Chiron), a
> >>> third-party basecaller still under development that uses a deeper neural
> >>> network than ONT’s basecallers [3].
> >>>> The third party basecaller Chiron's license is Mozilla Public License,
> >>> v. 2.0.
> >>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
> >>>>
> >>>
> >> --
> >> Michael R. Crusoe
>
--
http://fam-tille.de
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