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 It has some popcon number, but again it uses an outdated algorithm provided 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. > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de