Re: cufflinks

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Andreas Tille <andreas@xxxxxxxx> writes:

> Hi,
> On Wed, Jul 30, 2014 at 11:42:03AM +0100, Dave Love wrote:
>> > RNA-seq results by using TopHat and Cufflinks softwares.
>> cufflinks appears to be non-free, in which case it can't go into Fedora,
>> though there doesn't seem to have been a ruling from fedora-legal on it.
> The "non-free-ness" in Debian is caused by the use of locfit.

Yes <>

> So while the code is free software the restriction:
>  ... should not, and can not, be used to
>  derive meaningful benchmarks, either for the speed or accuracy of algorithms.
> is something what is regarded as non-free by Debian.

It's a restriction usage, if taken at face value, contra Freedom 0, in
which case it's not free software.

> I several times
> tried to contact the authors about this but never got any response.

I couldn't track down whoever seemed to be the relevant one, but I
didn't try too hard.  It's useful to know it's not worth the effort.  I
did get a response from the cufflinks maintainer, but I think the
missing licence file didn't get added to the cufflinks distribution.

> I'd be interested about the opinion of fedora-legal.

I can ask after I get back from holiday, unless someone else cares to.
I don't know if you need to be a Fedora developer to do that, though.

I had hoped it might be possible to set up a repo that could contain the
non-free things we have to install (abyss is another in this area).
Unfortunately the UK HPC community isn't interested in that sort of
thing -- or at least the people that matter -- and I don't have the
resources here.
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