I am willing to ask about guppy first, but what address could I use best? And I'm afraid that I will not be that convincing, don't know the exact use and needs for having guppy freed. 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 <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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