[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))

[Alex Mestiashvili]

>> 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 ...

I would leave such a change to upstream. There might be some 
publications or work using giira with tophat and it should be 
reproducible exactly with these tools (well versions are important too), 
it might be quite surprising that giira is suddenly using hisat and only 
in Debian.

> 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 It has some popcon number, but again it uses an outdated algorithm provided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.

Sure, let's wait.

Best regards,
Alex