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 t...@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 Fri, Apr 10, 2020 at 2:26 PM Andreas Tille <andr...@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 > > > > t...@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 <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 >
