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
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