Re: 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))
CC-ing Debian Med user list and specifically Tony to raise his
opinion from a BioLinux point of view. Tony, what's your point
about loosing software that can not be portet to Python3?
Kind regards, Andreas.
On Wed, Nov 27, 2019 at 12:03:13PM +0100, Andreas Tille wrote:
> 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 It has some popcon number, but again it uses an outdated algorithm provided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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> http://fam-tille.de
>
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