Andreas: If clustal, cufflinks, phylip, paml and many other bioinformatics packages are just fine in the non-free repo, couldn't we do the same with blat?
http://http.us.debian.org/debian/pool/non-free/c/ http://http.us.debian.org/debian/pool/non-free/e/ http://http.us.debian.org/debian/pool/non-free/p/ On Wed, Oct 25, 2017 at 1:59 PM, Jim Kent <[email protected]> wrote: > We attempted to get it into in the non-free section last time, and > that is where we still ran into problems where the Debian folks didn't > like our usual license, I went through a web site to find a standard > license for noncommercial use that they could agree with, and then > they couldn't work with what I'd found there for a reason that seemed > like a lawyer's or ontologist's nits, and it seemed like it would be a > time consuming and potentially expensive thing to find a solution that > would make everyone happy. > > At any rate, this current thread seems to be based on us no longer > charging for or restricting commercial use, which is false. Our > license is still same as ever. > > On Wed, Oct 25, 2017 at 1:23 PM, Maximilian Haeussler <[email protected]> > wrote: >> Is there any chance to get it into the non-free repo? >> >> Debian has other non-OSS software packages that it distributes as part >> of non-free. Why not BLAT? >> >> On Wed, Oct 25, 2017 at 1:06 PM, Andreas Tille <[email protected]> wrote: >>> Hi Kent, >>> >>> thanks for your quick reply. >>> >>> On Wed, Oct 25, 2017 at 11:44:02AM -0700, Jim Kent wrote: >>>> Hi - Blat does have it's own unique license. The essence of it is >>>> that it is free for personal, academic, and non-profit use, and >>>> requires a fee paying license from Kent Informatics for commercial >>>> use. I spent some time trying to find a standard license that fit a >>>> year or two ago, and then apparently it wasn't standard enough. I'm >>>> kind of reluctant to go through that exercise again. Is there no way >>>> you can use our very simple license for non-commercial users? >>> >>> I think I explained in the past in detail that *any* restriction for >>> *any* user makes the code non-free and can not distributed with Debian >>> (and in the same manner not with seqtools which is GPL-3). I had the >>> impression that you was willing to drop the non-profit use restriction >>> but it seems I was wrong. The reason that you did not found a standard >>> Open Source license is that your restriction is in conflict per >>> definition with Open Source licenses. >>> >>> I had this discussion with Joe Felsenstein for years and he finally >>> realised that the non-commercial restriction has more drawbacks (like >>> beeing not included in any Linux distribution) than advantages (really >>> low payment from commercial users ... are you sure that commercial >>> users really pay for a license in their closed products?) >>> >>> This idea has distributed quite widely in scientific software world >>> and may be you reconsider your decision. >>> >>> Kind regards >>> >>> Andreas. >>> >>>> On Wed, Oct 25, 2017 at 3:20 AM, Andreas Tille <[email protected]> >>>> wrote: >>>> > Hi again, >>>> > >>>> > I'm stumbling upon some definitive answer about the license of blatSrc >>>> > which can be found in several projects. My last hit was seqtools[1] >>>> > from Sanger which claims to be licensed as GPL-3 but as far as I can see >>>> > this would conflict with the licensing statement of the latest blatSrc >>>> > download I'm aware about[2]. So it would really help to get some >>>> > official statement under what license blatSrc can be used and where >>>> > to find the latest version. >>>> > >>>> > Thanks a lot >>>> > >>>> > Andreas. >>>> > >>>> > [1] http://www.sanger.ac.uk/science/tools/seqtools >>>> > [2] https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip >>>> > >>>> > On Sat, Sep 10, 2016 at 11:36:38PM +0200, Andreas Tille wrote: >>>> >> Hi again, >>>> >> >>>> >> I'd like to pick up the ball for blat again. For me it is not yet clear >>>> >> by what license blat is covered and what might be the role of the >>>> >> KentLib >>>> >> library[1] plays. Is it possible to link blat against KentLib and is it >>>> >> sensible to start packaging this first. >>>> >> >>>> >> Just to let you know: The freeze for the next Debian release is coming >>>> >> soon and it blat should be distributed with the next release we should >>>> >> hurry up to get this done. For me it remains unclear who is responsible >>>> >> for what and role the different pieces of code are playing. >>>> >> >>>> >> Kind regards >>>> >> >>>> >> Andreas. >>>> >> >>>> >> [1] https://github.com/jstjohn/KentLib >>>> >> >>>> >> On Thu, Feb 27, 2014 at 12:49:06AM -0800, Jim Kent wrote: >>>> >> > Yes. If you could reiterate some of the links, or if you prefer just >>>> >> > forward this whole thread to Hiram, it would be great. Then I can >>>> >> > go back >>>> >> > to wrestling with the ENCODE monster! >>>> >> > >>>> >> > >>>> >> > On Thu, Feb 27, 2014 at 12:31 AM, Andreas Tille <[email protected]> >>>> >> > wrote: >>>> >> > >>>> >> > > Hi Jim, >>>> >> > > >>>> >> > > seems like we got in contact to the perfectly right time. :-) >>>> >> > > >>>> >> > > I'm happily waiting for your colleagues showing up at the Debian Med >>>> >> > > list (which I'd strongly recommend for this purpose since I'm just a >>>> >> > > member of the team and not the whole team ;-)) and repeat that one >>>> >> > > of >>>> >> > > them might be interested in our Mentoring of the Month effort >>>> >> > > >>>> >> > > https://wiki.debian.org/DebianMed/MoM >>>> >> > > >>>> >> > > Looking forward to a great cooperation >>>> >> > > >>>> >> > > Andreas. >>>> >> > > >>>> >> > > On Thu, Feb 27, 2014 at 12:17:09AM -0800, Jim Kent wrote: >>>> >> > > > Disabling the pslCheck seems like the sensible and pragmatic >>>> >> > > > thing. >>>> >> > > > >>>> >> > > > I'm going to write a short note introducing you to Hiram Clawson, >>>> >> > > > and >>>> >> > > also >>>> >> > > > Ann Zweig our project manager (and Hiram's boss). It is actually >>>> >> > > > part of >>>> >> > > > our grant to package the tools in ways to make it easier for >>>> >> > > > people to >>>> >> > > use >>>> >> > > > them. Our current system is not so bad, but it requires people >>>> >> > > > to >>>> >> > > > actually read the README, and set an environment variable. This >>>> >> > > > was >>>> >> > > state >>>> >> > > > of the art in 1985, but not the >>>> >> > > > config >>>> >> > > > make >>>> >> > > > make install >>>> >> > > > people are used to these days, never mind a RPM or anything more >>>> >> > > > recent, >>>> >> > > > and most of the younger programmers get lost. >>>> >> > > > >>>> >> > > > I do think we want to do some renaming of directories and the >>>> >> > > > like as >>>> >> > > part >>>> >> > > > of this process, and ideally end up with all the code that is >>>> >> > > > under one >>>> >> > > > license under the same subdirectory. It's somewhat close to >>>> >> > > > that, but >>>> >> > > > there are enough exceptions to be a pain. We switched from CVS >>>> >> > > > to git >>>> >> > > > about 2 years ago in large part to make moving directories around >>>> >> > > > much >>>> >> > > less >>>> >> > > > of a pain in the butt, so we _can_ do this now, but it's been >>>> >> > > > sort of a >>>> >> > > > back burner thing, and is only about 10% complete. >>>> >> > > > >>>> >> > > > Anyway, we are paid by the taxpayers to do this sort of work, >>>> >> > > > and will >>>> >> > > > make some time for it. We would welcome your help, and getting >>>> >> > > > it into >>>> >> > > > Debian is as good a starting point as any, better than most if >>>> >> > > > we have >>>> >> > > > support from that group. >>>> >> > > > >>>> >> > > > Take care, >>>> >> > > > Jim >>>> >> > > > >>>> >> > > > >>>> >> > > > >>>> >> > > > On Wed, Feb 26, 2014 at 11:16 PM, Andreas Tille <[email protected]> >>>> >> > > wrote: >>>> >> > > > >>>> >> > > > > Hi Jim, >>>> >> > > > > >>>> >> > > > > On Wed, Feb 26, 2014 at 10:33:59PM -0800, Jim Kent wrote: >>>> >> > > > > > I'm glad you isolated it to the -O2. >>>> >> > > > > >>>> >> > > > > :-) >>>> >> > > > > >>>> >> > > > > > I don't think there's a super easy way to cut pslCheck out of >>>> >> > > > > > the >>>> >> > > whole >>>> >> > > > > > 1,200,000 UCSC genomics source tree. >>>> >> > > > > >>>> >> > > > > For the moment I simply disabled this check. I guess it is >>>> >> > > > > also this >>>> >> > > > > way sufficient to detect potential problems (and it was not the >>>> >> > > pslCheck >>>> >> > > > > that failed in the first place). >>>> >> > > > > >>>> >> > > > > > I would, on the other hand, be very >>>> >> > > > > > happy for you to take on the job of packaging up that whole >>>> >> > > > > > source >>>> >> > > tree >>>> >> > > > > for >>>> >> > > > > > Debian. I could refer you to a less busy member of my >>>> >> > > > > > staff, Hiram >>>> >> > > > > > Clawson, who has a _lot_ of experience helping people get >>>> >> > > > > > that to >>>> >> > > build. >>>> >> > > > > >>>> >> > > > > This is a very cool offer. I actually have thought about >>>> >> > > > > packaging the >>>> >> > > > > whole UCSC genomics source tree as well since it obviously >>>> >> > > > > contains >>>> >> > > > > several tools that perfectly fit in our scope. I wonder >>>> >> > > > > whether Hiram >>>> >> > > > > might even like to learn something about Debian packaging. In >>>> >> > > > > our team >>>> >> > > > > we have quite some tradition in mentoring people as you can see >>>> >> > > > > here: >>>> >> > > > > >>>> >> > > > > https://wiki.debian.org/DebianMed/MoM >>>> >> > > > > >>>> >> > > > > Perhaps it comes handy if somebody in your team is capable to >>>> >> > > > > create >>>> >> > > > > Debian packages which in the end is not more than wrapping up >>>> >> > > > > the build >>>> >> > > > > process into some sceme. >>>> >> > > > > >>>> >> > > > > BTW, when I inspected the jksrc source tree (and also in the >>>> >> > > > > specific >>>> >> > > > > case of the blat source) I realised that it might make real >>>> >> > > > > sense to >>>> >> > > > > enable dynamic linking of the tools against the static >>>> >> > > > > libraries you >>>> >> > > are >>>> >> > > > > creating. The Debian way to do this would be to create two >>>> >> > > > > packages: >>>> >> > > > > >>>> >> > > > > lib<name> containing the dynamic libraries >>>> >> > > > > lib<name>-dev containing the static libraries and header >>>> >> > > > > files >>>> >> > > > > >>>> >> > > > > To approach this easily it is quite convenient to use either GNU >>>> >> > > > > automake or cmake (at your preference) since these build >>>> >> > > > > systems easily >>>> >> > > > > support the creation of dynamic and static libraries in >>>> >> > > > > parallel. This >>>> >> > > > > would also simplify the hancling of MACHTYPE in your makefiles >>>> >> > > > > since >>>> >> > > > > these Build systems are capable to handle this automatically. >>>> >> > > > > In >>>> >> > > short: >>>> >> > > > > before we might start packaging the whole source tree it would >>>> >> > > > > be quite >>>> >> > > > > sensible to switch to an advanced build system which would be >>>> >> > > > > also in >>>> >> > > > > your profit at the end. >>>> >> > > > > >>>> >> > > > > > The licensing of it is quite complex alas. There are three >>>> >> > > > > > main >>>> >> > > parts: >>>> >> > > > > > >>>> >> > > > > > - a small part which is owned by me in a directory called >>>> >> > > > > > jkOwnLib, >>>> >> > > and >>>> >> > > > > in >>>> >> > > > > > the blat directories >>>> >> > > > > >>>> >> > > > > This would probably make a separate library package. However, >>>> >> > > > > you >>>> >> > > might >>>> >> > > > > consider a name which is more descriptive than jkOwnLib. >>>> >> > > > > >>>> >> > > > > > - a medium sized part that contains stuff we regard as >>>> >> > > > > > generally >>>> >> > > useful >>>> >> > > > > > which is essentially public domain, but that we are happy >>>> >> > > > > > distributed >>>> >> > > > > under >>>> >> > > > > > a BSD or MIT license >>>> >> > > > > >>>> >> > > > > Cool. That would be very interesting. >>>> >> > > > > >>>> >> > > > > > - a large part that is genomics in general, and UCSC Genome >>>> >> > > > > > Browser >>>> >> > > in >>>> >> > > > > > particular specific that is owned by UCSC and has a license >>>> >> > > > > > much like >>>> >> > > > > blat >>>> >> > > > > > - free for personal, academic, and non-profit use, and >>>> >> > > > > > requiring a >>>> >> > > > > license >>>> >> > > > > > for commercial use. In this case the licence needs to come >>>> >> > > > > > from UCSC >>>> >> > > > > > (contact Will Hale) rather than Kent Informatics (contact >>>> >> > > > > > Heidi >>>> >> > > > > Brumbaugh). >>>> >> > > > > >>>> >> > > > > In case we have a good plan about the technical details we >>>> >> > > > > should >>>> >> > > > > probable contact these persons regarding the licensing. >>>> >> > > > > >>>> >> > > > > Kind regards >>>> >> > > > > >>>> >> > > > > Andreas. >>>> >> > > > > >>>> >> > > > > -- >>>> >> > > > > http://fam-tille.de >>>> >> > > > > >>>> >> > > >>>> >> > > -- >>>> >> > > http://fam-tille.de >>>> >> > > >>>> >> >>>> >> -- >>>> >> http://fam-tille.de >>>> >> >>>> >> >>>> > >>>> > -- >>>> > http://fam-tille.de >>>> >>> >>> -- >>> http://fam-tille.de
