Hi Ben, On Tue, Apr 28, 2020 at 03:16:56PM +0200, Ben Tris wrote: > I am willing to ask about guppy first,
Thanks a lot. > but what address could I use best? May be you can check out the links Michael has given. Does anybody have some other points of contact? I personally have no idea, sorry. > And I'm afraid that I will not be that convincing, don't know the > exact use and needs for having guppy freed. I'd start with the fact that guppy is on our list of software that is relevant to fight COVID-19. At the end of our wiki page https://wiki.debian.org/DebianMed/SoftwareLiberation is a nice link about kallisto featuring good arguments. Hope this helps Andreas. > On 28-04-20 15:11, Andreas Tille wrote: > > 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 <[email protected]> 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 <[email protected]> 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
