Re: Please choose a free license for gmap
Hi Thomas,
sorry, it was my fault - the URL is surely coded in our (formerly)
non-free package. I just messed gmap up with gblocks where author
is missing.
Thanks a lot - I've just uploaded the latest version to Debian
new queue to be accepted for main.
Kind regards and thanks for considering a free license
Andreas.
On Fri, Apr 10, 2020 at 03:31:09PM -0700, Thomas Wu wrote:
> All source code is available at
>
> http://research-pub.gene.com/gmap
>
> The version starting with 2019-12-01 is open source. The most recent
> version is 2020-04-08.
>
> Thanks,
>
> Tom
>
>
>
> Thomas D. Wu, M.D., Ph.D.
>
> Principal Scientist, Bioinformatics & Computational Biology
>
> Genentech <https://www.gene.com/>, A Member of the Roche Group
>
> Office +1 (650) 225-5672
>
> twu@gene.com
>
> Join Genentech on LinkedIn <https://www.linkedin.com/company/genentech> |
> Twitter
> <https://twitter.com/genentech?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor>
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> <https://www.instagram.com/genentech/?hl=en> | YouTube
> <https://www.youtube.com/genentech>
>
>
>
> On Fri, Apr 10, 2020 at 2:26 PM Andreas Tille <andreas@an3as.eu> wrote:
>
> > Hi Tom,
> >
> > thanks a lot for this helpful hint. Yes, it is definitely relevant.
> > Do you have any link to the source code?
> >
> > Kind regards
> > Andreas.
> >
> > On Fri, Apr 10, 2020 at 10:42:15AM -0700, Thomas Wu wrote:
> > > Hi Andreas,
> > >
> > > It has taken a couple of years, and I don't know if it's relevant any
> > more,
> > > but GMAP and GSNAP are now released as open source under the Apache 2.0
> > > license.
> > >
> > > Thanks,
> > >
> > > Tom
> > >
> > >
> > > Thomas D. Wu, M.D., Ph.D.
> > >
> > > Principal Scientist, Bioinformatics & Computational Biology
> > >
> > > Genentech <https://www.gene.com/>, A Member of the Roche Group
> > >
> > > Office +1 (650) 225-5672
> > >
> > > twu@gene.com
> > >
> > > Join Genentech on LinkedIn <https://www.linkedin.com/company/genentech>
> > |
> > > Twitter
> > > <
> > https://twitter.com/genentech?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor
> > >
> > > | Facebook <https://www.facebook.com/Genentech/> | Instagram
> > > <https://www.instagram.com/genentech/?hl=en> | YouTube
> > > <https://www.youtube.com/genentech>
> > >
> > >
> > >
> > > On Mon, Jul 16, 2018 at 11:27 PM Andreas Tille <andreas@fam-tille.de>
> > wrote:
> > >
> > > > Hi again Thomas,
> > > >
> > > > since I was checking the new version of gmap I also checked whether the
> > > > promising message of yours from Sep 05, 2017 regarding a licens change
> > > > might be realised. I have not seen any change in the COPYING file. Do
> > > > you keep on considering choosing a free license?
> > > >
> > > > I have also a technical question: It seems, version 2018-07-04 does not
> > > > build the library any more by default. I'm not a user of this software
> > > > nor the library in special (just checked the packaging which fails now
> > > > since the lib is not build). Does this mean the library is not
> > > > supported / recommended any more and we should drop that binary package
> > > > or is there just a new switch for configure (I tried --enable-lib but
> > > > failed) we need to use?
> > > >
> > > > Kind regards
> > > >
> > > > Andreas.
> > > >
> > > > On Wed, Feb 28, 2018 at 10:33:01AM +0100, Alex Mestiashvili wrote:
> > > > > Dear Thomas,
> > > > >
> > > > > Taking into account the major rewrite of GMAP and GSNAP, I wonder if
> > you
> > > > > could consider the license change as well?
> > > > >
> > > > > Thank you,
> > > > > Alex, on behalf of Debian-Med.
> > > > >
> > > > > On 09/05/2017 10:51 PM, Andreas Tille wrote:
> > > > > > Hi Thomas,
> > > > > >
> > > > > > thanks for you fast and positive response. Feel free to contact
> > our
> > > > > > mailing list in case you might face problems. We have some
> > experience
> > > > > > in licensing questions.
> > > > > >
> > > > > > Kind regards
> > > > > >
> > > > > > Andreas.
> > > > > >
> > > > > > On Tue, Sep 05, 2017 at 10:01:40AM -0700, Thomas Wu wrote:
> > > > > >>
> > > > > >> Hi Alex,
> > > > > >>
> > > > > >> Thanks for your note. It's something I will consider. In fact,
> > our
> > > > > >> previous department head, Robert Gentleman, was the author of the
> > R
> > > > > >> statistical package, and thought we should do this. However, he
> > left
> > > > > >> our company some time ago, and we are still looking for a
> > department
> > > > > >> head.
> > > > > >>
> > > > > >> I would also have to consult with our legal department, since the
> > > > > >> software was built using company resources and on company time.
> > > > > >>
> > > > > >> Regards,
> > > > > >>
> > > > > >> Tom
> > > > > >>
> > > > > >> --
> > > > > >> Thomas D. Wu, M.D., Ph.D.
> > > > > >> Principal Scientist, Bioinformatics & Computational Biology
> > > > > >> Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
> > > > > >> Phone: 650-225-5672, Fax: 650-225-5389
> > > > > >> E-mail: twu@gene.com
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> On Mon, Sep 04, 2017 at 04:25:50PM +0200, Alex Mestiashvili wrote:
> > > > > >>> Hi,
> > > > > >>>
> > > > > >>> I'm writing you on behalf of the Debian Med team which is a group
> > > > inside
> > > > > >>> Debian with the objective to package free software with
> > relevance in
> > > > > >>> biology and medicine for official Debian. As you might possibly
> > > > know we
> > > > > >>> have created packages also from gmap as you can see on our so
> > > > > >>> called tasks biology page[1].
> > > > > >>>
> > > > > >>> According to the Debian Free Software Guidelines[2] which are
> > widely
> > > > > >>> accepted as Open Source definition the current license is not
> > free
> > > > since
> > > > > >>> it forbids the use and distribution of modified copy under some
> > > > > >>> conditions and also forbids free use of the software in
> > commercial
> > > > products.
> > > > > >>>
> > > > > >>> I wonder whether you might consider changing the licensing to
> > some
> > > > free
> > > > > >>> license like GPL, BSD or MPL - just anything that has no such
> > > > > >>> restriction to non-commercial use and use of modified code. You
> > > > might
> > > > > >>> like to know that several other authors of biologic software
> > recently
> > > > > >>> switched to free licenses (may be most prominently phylib). The
> > > > > >>> advantage for you inside Debian would be a higher visibility of
> > gmap
> > > > > >>> (since we distribute it with metapackages) and a way better
> > quality
> > > > > >>> assurance since Debian is running several tools to automatically
> > > > detect
> > > > > >>> problems inside the distributed software.
> > > > > >>>
> > > > > >>>
> > > > > >>> Kind regards and thanks for your cooperation
> > > > > >>>
> > > > > >>> Alex
> > > > > >>>
> > > > > >>> [1] http://blends.debian.org/med/tasks/bio#gmap
> > > > > >>> [2] https://www.debian.org/social_contract#guidelines
> > > > > >>>
> > > > > >> End of quote
> > > > > >>
> > > > > >>
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > http://fam-tille.de
> > > >
> > > >
> >
> > --
> > http://fam-tille.de
> >
--
http://fam-tille.de
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