Re: Packaging BLAT for Debian
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 <andreas@an3as.eu> 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 <andreas@fam-tille.de> 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 <tille@debian.org> 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 <tille@debian.org>
>> >> > > 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
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