Hi Yozen,
more than one year ago and one Debian release later I'd like to refresh
my question: Do you have any news about freeing Tandem Repeat Finder?
Kind regards
Andreas.
--
On Wed, Jun 22, 2016 at 11:02:28AM +0200, Andreas Tille wrote:
> Hi Yozen,
>
> thanks for your hint and understanding - I'll write to Gary Benson.
>
> Kind regards
>
> Andreas.
>
> On Sun, Jun 19, 2016 at 12:12:55PM -0400, Yozen Hernandez wrote:
> > Dear Michael and the rest of the Debian Medical Team,
> >
> > Sorry again for the long response time. I should clarify that I am only the
> > current maintainer of TRF, and have no say over whether or not it becomes
> > open source. For further inquiries regarding TRF, please contact the
> > original author, and my PI, Dr Gary Benson at gbenson@bu.edu.
> >
> > As for all of your arguments regarding the importance of open source
> > software, especially in science, please know that I completely agree with
> > you on every point. I am personally a strong supporter of open source
> > software, and everything that I write myself I either have released, or
> > plan to release under an open source license.
> >
> > Thanks for all your interest.
> >
> > Best,
> > Yozen
> >
> >
> > *Yözen Hernández*
> > *Graduate Program in Bioinformatics, PhD Candidate*
> > *Laboratory for Biocomputing and Informatics*
> > *Boston University*
> > *(347) 829-6936 - [ (347) 82YOZEN ]*
> >
> > On Fri, May 27, 2016 at 4:31 AM, Michael Crusoe <michael.crusoe@gmail.com>
> > wrote:
> >
> > > Dear Yozen,
> > >
> > > As a research software engineer who works with sequencing analysis
> > > researchers I join Andreas in asking you to release Tandem Repeat
> > > Finder under a free license.
> > >
> > > I see that you have been funded with NSF grants, that is great!
> > > However, to treat the public ethically, the software should be free—as
> > > in freedom—for the whole public. This means the freedom to read the
> > > source code so that they may understand it better, the freedom to
> > > modify the source code so that they may improve upon it, and the
> > > freedom to redistribute the source code and their modifications so
> > > that they may share bug fixes and new features.
> > >
> > > Many researchers actively avoid non-open-source software, see a
> > > discussion from my previous boss C. Titus Brown:
> > > http://ivory.idyll.org/blog/2015-on-licensing-in- bioinformatics.html
> > > under "Why avoid non-open-source software?"
> > >
> > > One of the many benefits I have enjoyed with releasing my software
> > > under a free or open source license is the improvements I get from
> > > other users.
> > >
> > > TRF is widely used, as I'm sure you know. Unlike most software that
> > > has been written it has shown to be useful. Sharing the source code
> > > provides a path to sustainability should you decide to dedicate your
> > > time to other projects or if you are not able to continue maintaining
> > > the codebase.
> > >
> > > I hope you take my letter into consideration. If you have any
> > > questions about licensing I would be happy to answer them.
> > >
> > > This is not an obligation to run a community based open source
> > > project, we're just asking for the right to further redistribute your
> > > work (with prominent attribution!) so that more people can use it.
> > >
> > > Cheers,
> > >
> > > On Sun, May 15, 2016 at 9:46 AM, Andreas Tille <tille@debian.org> wrote:
> > > > Hi Yozen,
> > > >
> > > > On Thu, May 12, 2016 at 08:11:53PM -0400, Yozen Hernandez wrote:
> > > >> Dear Andreas,
> > > >>
> > > >> Thank you for contacting about packaging TRF. I indeed missed your
> > > email.
> > > >>
> > > >> Unfortunately, the source code for TRF is not freely available. I do not
> > > >> know the Debian Free Software Guidelines well enough to decide whether
> > > or
> > > >> not this is allowed,
> > > >
> > > > The Debian Free Software Guidelines[1] are widely accepted as Open
> > > > Source definition and it is actually that the source code is freely
> > > > available.
> > > >
> > > >> but I may have a solution that I have seen other
> > > >> packages use. For instance, the Oracle Java packages I have seen ask the
> > > >> user to accept a license agreement. The package script then goes on to
> > > >> download the appropriate binary upon acceptance. This could be part of
> > > the
> > > >> RepeatMasker package since TRF is required by that software, and I can
> > > >> assist by providing the URLs for the i386 and x64 builds.
> > > >
> > > > There are several glitches in this suggestion:
> > > >
> > > > 1. The Oracle Java packages are not part of Debian. Debian ships
> > > > with OpenJDK. In so far the comparison is weak.
> > > > 2. For official Debian packages there is no point to ask for a
> > > > license since the user can be sure that the installed software
> > > > is per definition free.
> > > > 3. Debian packages can only depend from other Debian packages
> > > > but not from unofficial ones like Oracle Java or your suggested
> > > > TRF
> > > > 4. Debian ships for several architectures not only i386 and x64 (in
> > > > Debian nomenclature amd64). For instance architectures like arm64
> > > > and ppc64 might become quite interesting in the near future and
> > > > we try to care for building on these architectures as well
> > > >
> > > > So far for the general considerations. In the specific case of
> > > > scientific software we also consider the free availability of the source
> > > > code as very important to prove the correctness of the results and
> > > > enable reproducibility. So in this case there are extra good reasons
> > > > for publishing the code.
> > > >
> > > >> Another work around could be to ask the user to manually download and
> > > >> install TRF themselves by providing them with the URL to our downloads
> > > page.
> > > >
> > > > As said above a Debian package is not allowed to depend from external
> > > > resources.
> > > >
> > > >> I understand that these are not ideal solutions, but for the forseeable
> > > >> future we will not license TRF under a free software license.
> > > >
> > > > I have no idea whether this might be open for discussion at your site
> > > > and what might be the motivation to keep the code of a scientific tool
> > > > closed. In case you might like to re-think it I'd like to point out
> > > > the following advantages:
> > > >
> > > > Due to the work of the Debian Med team Debian and its derivatives like
> > > > Ubuntu gained quite some coverage in biological research. Providing TRF
> > > > via Debian packages does not only simplify the installation and
> > > > maintenance for users (you might keep cluster installations in mind).
> > > >
> > > > The fact that we are providing so called metapackages depending from all
> > > > biological applications installing any application you see on this so
> > > > called tasks page[2] might bring TRF automatically on users computers
> > > > who might become aware of your tool just because it is included here and
> > > > you might gain additional users of your software.
> > > >
> > > > As you can see on the tasks page[2] we also put some importance on
> > > > specifying the according publications which gives the authors of the
> > > > software some extra credit.
> > > >
> > > > I could give several more good reasons but I don't know your motivation
> > > > to keep the source code closed and may be you could rethink the decision
> > > > by including the arguments above.
> > > >
> > > > Kind regards
> > > >
> > > > Andreas.
> > > >
> > > > [1] https://www.debian.org/social_contract#guidelines
> > > > [2] http://blends.debian.org/med/tasks/bio
> > > >
> > > > --
> > > > http://fam-tille.de
> > > >
> > >
> > >
> > >
> > > --
> > > Michael R. Crusoe
> > > Community Engineer & Co-founder
> > > Common Workflow Language project
> > > https://impactstory.org/u/0000-0002-2961-9670
> > > michael.crusoe@gmail.com
> > > +32 (0) 2 808 25 58
> > > +1 480 627 9108
> > >
>
> --
> http://fam-tille.de
>
>
http://fam-tille.de