[Debian-med-packaging] Removing tophat (Was: Bug#938677: Please check autopkgtest of (may be failed) attempt of Python3 port (Was: Bug#938677: tophat: Python2 removal in sid/bullseye))

[Andreas Tille]

On Wed, Nov 27, 2019 at 10:21:42AM +0100, Alex Mestiashvili wrote:
> Before removing tophat I guess we need to handle the reverse deps:
>   med-bio
>   cufflinks
>   giira
>   med-cloud
> 
> med-bio and med-cloud just need to remove the tophat from the list.

We can easily release new med-* metapackages.

> cufflinks doesn't depend on Tophat, just enchances it.
> 
> So there is only giira which will suffer from tophat's removal, but it is
> also a 5 years old code never updated by upstream.

My guess it will also not get any update.  Grepping the source:

src/geneFinder/ReadInParameters_GeneFinder.java:                                " \n -mT [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat \n" +
src/geneFinder/TopHat_Call.java:                for(File readFile : GeneFinder.rnaFilesWithNames.keySet()){     // if there is more than one read file, report them to tophat in a list
src/geneFinder/TopHat_Call.java:                        secondExe = "tophat2 --no-sort-bam " + optionString + "-o " + out_dir + " " + nameRefFile + " " + rnaFile;
src/geneFinder/TopHat_Call.java:                        secondExe = "tophat2 --no-sort-bam " + optionString + "-o " + out_dir + " " + nameRefFile + " " + fileNames;
src/geneFinder/GeneFinder.java:                                 TopHat_Call tophatStart = new TopHat_Call();
src/geneFinder/GeneFinder.java:                                 tophatStart.callTopHat(nameRef);

It even looks as if we could replace tophat by hisat there ...
Currently popcon shows 5 votes which is half the number of tophat.  Not
sure whether giira itself is triggering votes for tophat.  If we might
get some explicite vetos for giira here it might be worth to try
replacing the tophat call by a hisat2 call - otherwise we probably will
not loose much it it is removed as well.

> It has some popcon number, but again it uses an outdated algorithm provided
> by tophat which is not maintained anymore.
> 
> Shall I open bugs against the reverse dependencies asking to remove tophat?
> Could you please advise with the common procedure for that?

I think we simply wait for some veto for a giira removal here and
act accordingly.  Meanwhile I can re-render debian-med metapackages.

Kind regards

       Andreas.

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