Re: Fasta3 is non-free just because of some Smith Waterman implementation (Was: Please choose a free license for fasta3 components)
Hi again, any progress with this? Kind regards Andreas. On Fri, Sep 06, 2019 at 09:51:28AM +0200, Alex Mestiashvili wrote: > Thanks Erik! > > I'll try to get in touch with upstream and inform them that the code is > actually free. > However, while packaging of swsse2 makes sense, the source code is not > providing drop-in replacement for the code in fasta3. Nevertheless the > upstream of fasta3 can change the license anyway as far as I understand. > > Best, > Alex > > > On 9/6/19 9:22 AM, Andreas Tille wrote: > > Hi, > > > > beside the sad issue: Is someone taking over the packaging of the code > > and did you talked with fast3 upstream that the code is actually free? > > > > Kind regards > > > >Andreas. > > > > On Tue, Aug 20, 2019 at 02:39:05PM +0200, Steffen Möller wrote: > >> That is truly sad, indeed. Many thanks go to his widow and to Prof. Eddy > >> for caring. It is also an opportunity to think about how we as a > >> community can grow. A donation box for instance would never be enough to > >> feed the kids, but it would be something like a nice gesture about work > >> and his creator not being forgotten. We should possibly bring this up at > >> our next Sprint. > >> > >> Thank for this pointer, Erik. > >> > >> Steffen > >> > >> On 20.08.19 11:07, Erik Sjölund wrote: > >>> Hi Andreas, > >>> > >>> Regarding "Alex has once contacted upstream" note the sad news from > >>> https://cryptogenomicon.org/2019/03/11/farrars-striped-simd-smith-waterman/ > >>> > >>> Kind regards, > >>> Erik > >>> > >>> On Mon, Aug 19, 2019 at 10:06 PM Andreas Tille wrote: > Hi Steffen, > > you have uploaded fasta3. When I wanted to upgrade to latest upstream I > realised that it is in non-free just because of two files implementing a > Smith Waterman algorithm. Alex has once contacted upstream as you can > see on our SoftwareLiberation page[1]. At least the wiki page does not > state any response. > > I wonder whether you might try to ping upstream or possibly use libssw > or libsmithwaterman as a replacement. > > Kind regards > > Andreas. > > [1] https://wiki.debian.org/DebianMed/SoftwareLiberation > > -- > http://fam-tille.de > > >> > >> > > > > -- http://fam-tille.de
Re: Fasta3 is non-free just because of some Smith Waterman implementation (Was: Please choose a free license for fasta3 components)
Hi Andreas, Unfortunately I didn't get any answer, here is the mail I've sent to the upstream. https://lists.debian.org/debian-med/2019/09/msg00039.html May be you or Steffen would like to try your luck, who knows, may be my email went to spam or something like that. Regards, Alex On 1/6/20 2:11 PM, Andreas Tille wrote: > Hi again, > > any progress with this? > > Kind regards > >Andreas. > > On Fri, Sep 06, 2019 at 09:51:28AM +0200, Alex Mestiashvili wrote: >> Thanks Erik! >> >> I'll try to get in touch with upstream and inform them that the code is >> actually free. >> However, while packaging of swsse2 makes sense, the source code is not >> providing drop-in replacement for the code in fasta3. Nevertheless the >> upstream of fasta3 can change the license anyway as far as I understand. >> >> Best, >> Alex >> >> >> On 9/6/19 9:22 AM, Andreas Tille wrote: >>> Hi, >>> >>> beside the sad issue: Is someone taking over the packaging of the code >>> and did you talked with fast3 upstream that the code is actually free? >>> >>> Kind regards >>> >>>Andreas. >>> >>> On Tue, Aug 20, 2019 at 02:39:05PM +0200, Steffen Möller wrote: That is truly sad, indeed. Many thanks go to his widow and to Prof. Eddy for caring. It is also an opportunity to think about how we as a community can grow. A donation box for instance would never be enough to feed the kids, but it would be something like a nice gesture about work and his creator not being forgotten. We should possibly bring this up at our next Sprint. Thank for this pointer, Erik. Steffen On 20.08.19 11:07, Erik Sjölund wrote: > Hi Andreas, > > Regarding "Alex has once contacted upstream" note the sad news from > https://cryptogenomicon.org/2019/03/11/farrars-striped-simd-smith-waterman/ > > Kind regards, > Erik > > On Mon, Aug 19, 2019 at 10:06 PM Andreas Tille wrote: >> Hi Steffen, >> >> you have uploaded fasta3. When I wanted to upgrade to latest upstream I >> realised that it is in non-free just because of two files implementing a >> Smith Waterman algorithm. Alex has once contacted upstream as you can >> see on our SoftwareLiberation page[1]. At least the wiki page does not >> state any response. >> >> I wonder whether you might try to ping upstream or possibly use libssw >> or libsmithwaterman as a replacement. >> >> Kind regards >> >>Andreas. >> >> [1] https://wiki.debian.org/DebianMed/SoftwareLiberation >> >> -- >> http://fam-tille.de >> >>> >> >> >
debianmed sprint hotel
Hi, has anyone made an hotel choice for the sprint so that we can start reservertions to be together if possible? We could also possibly share some room. Olivier -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
