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Re: Please provide source code for Tandem Repeats Finder under a freely redistributable license

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:
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.


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
+32 (0) 2 808 25 58
+1 480 627 9108

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