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

[Andreas Tille <tille@debian.org>]

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.

Kind regards

       Andreas.

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
> 
> 
> 
> On Mon, Apr 27, 2020 at 2:58 PM Andreas Tille <tille@debian.org> wrote:
> 
> > Hi,
> >
> > I also tried my luck to find the source code for guppy base caller - but
> > failed.  It would of great help if somebody could find out.
> >
> > Thanks a lot Jun for giving detailed hints so far
> >
> >      Andreas.
> >
> > On Fri, Apr 24, 2020 at 08:41:22PM +0200, Jun Aruga wrote:
> > > > >
> > https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> > > > > guppy
> > > > Missing in Debian.  Is it this project
> > > >    https://staff.aist.go.jp/yutaka.ueno/guppy/  ?
> > >
> > > Hi, Andreas,
> > > No, it seems that guppy is a base caller provided by Oxford Nanopore
> > > technologies.
> > >
> > > ```
> > > $ pwd
> > > /home/jaruga/git/nf-core/nanoseq
> > >
> > > $ grep -r guppy *
> > > ...
> > > conf/base.config:      container = 'genomicpariscentre/guppy-gpu:3.4.4'
> > > conf/base.config:      container = 'genomicpariscentre/guppy:3.4.4'
> > > ...
> > >
> > > Then check the containers Dockerfile.
> > >
> > > https://hub.docker.com/r/genomicpariscentre/guppy/dockerfile
> > > > wget -q
> > https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~xenial_amd64.deb
> > >
> > > https://hub.docker.com/r/genomicpariscentre/guppy-gpu/dockerfile
> > > > wget -q
> > https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${PACKAGE_VERSION}-1~xenial_amd64.deb
> > > ```
> > >
> > > It might not be open source software, seeing the following page.
> > > Here is a user's page about guppy in Japanese. I could not find the
> > > English page.
> > > You can see the guppy's screen shot on
> > > https://community.nanoporetech.com/downloads page.
> > >
> > > http://kazumaxneo.hatenablog.com/entry/2020/01/19/145940
> > >
> > > > Thanks again Jun for your very helpful contribution
> > >
> > > You are welcome. Let me comment on your comments later.
> > >
> > > Cheers,
> > > Jun
> > >
> > > --
> > > Jun | He - His - Him
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >
> >
> 
> -- 
> Michael R. Crusoe

-- 
http://fam-tille.de