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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)



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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