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
>
> t...@gene.com
>
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>
> On Mon, Jul 16, 2018 at 11:27 PM Andreas Tille <andr...@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: t...@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
