Re: removing tophat from Debian

[Steffen Möller <steffen_moeller@gmx.de>]

On 21.12.17 04:41, Afif Elghraoui wrote:
> On December 20, 2017 5:17:20 AM EST, Michael Crusoe <michael.crusoe@gmail.com> wrote:
> > 2017-12-16 10:18 GMT+02:00 Afif Elghraoui <afif@debian.org>:
> >
> > > Hi, all,
> > >
> > > Given the statement from the website [1]
> > >
> > > > Please note that TopHat has entered a low maintenance, low support
> > > > stage as it is now largely superseded by HISAT2 which provides the
> > > > same core functionality (i.e. spliced alignment of RNA-Seq reads),
> > > > in a more accurate and much more efficient way
> > This statement is about TopHat 2, which is what is in the Debian
> > package
> > tophat
> >
> >
> > > and a statement from one of its co-authors [2]
> > >
> > > > Please stop using Tophat. Cole and I developed the
> > > > method in *2008*. It was greatly improved in TopHat2 then HISAT
> > > > & HISAT2. There is no reason to use it anymore. I have been
> > > > saying this for years yet it has more citations this year than last
> > This more strongly worded statement is about TopHat 1, which is not in
> > Debian.
> The summary of the statement is that hisat2 is the only one of those 4 that isn't obsolete, and therefore that it's the only one of those 4 that should be used.
>
> > We should retain TopHat2, perhaps with a note about HISAT2.
> I think tophat2 (and hisat1 if we have it) should also be removed. We should get upstream involved if you still disagree.

So, what could justify a deprecated piece of software in Debian. To mind 
come:

 * an API change
 * a well-established tutorial that was not yet updated
 * historic landmarks achieved by that software that one wants to 
compare new developments against
 * pop-con

I have difficulties with the role of our distribution as some kind of 
package-value police. My personal
threshold for sponsoring is a peer-reviewed publication. But I like the 
role of our distribution as a communicator.
And we should indeed collect ideas on how to spread the news on a better 
alternative - any clear cut
improvals are rare enough, though.

If upstream explicitly asks for a removal from our distribution, then I 
am still hesitating. Do they also
retract their publication? Most likely not since at some point in 
history that previous version was just
fine. It is a document that we do not want to lose. The same for the 
software of that time. And I argue
that I do not want to lose the package, either. I am afraid that when we 
have it in snapshot.d.o, one or two
releases down the road, the package will be forgotten. We would need 
something in our task pages,
then, to point to it, I suggest.

Best,

Steffen