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Re: removing tophat from Debian

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 stage as it is now largely superseded by HISAT2 which provides the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.

We should retain TopHat2, perhaps with a note about HISAT2.

I think we'd be doing users a favor by removing it from the archive. If
in the future anyone wants to replicate old results based on tophat,
they could build a container off of snapshot.debian.org.

Are there any objections?


1. https://ccb.jhu.edu/software/tophat/index.shtml
2. https://twitter.com/lpachter/status/937055346987712512

Afif Elghraoui | عفيف الغراوي

Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project
Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania

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