Hi, Le 15/11/2020 à 18:16, Andreas Tille a écrit : > >> >> This may be worth a sidenote - bcbio to me is something metaphorical. We >> have it in the distribution already. And now we work to get all the >> runtime-dependencies in to make it functional. And snpEff is pretty high >> up (it interprets the importance of nucleotide variations, you need to >> have identified these variants for that, first). So, my comment on >> "snpeff" being invoked was to be interpreted as "see, here we are already". > > Snpeff is wanted from several sided. I really hope we get it soon. >
It's good we talk about it. There were 4 identified missing packages to be able to complete the packaging of Snpeff; 3 of them are now in Debian, only akka-actor misses. akka-actor is part of akka, this is a framework for concurrent programming written in Scala. And here is the problem: we have Scala 2.11 in Debian, current upstream version is 2.13 and akka would need at least 2.12. Also, Scala 2.12 and 2.13 would need Scala Build Tool (sbt) in order to be built, and sbt in turns requires Scala 2.12 or 2.13. I guess at some point, this loop did not exist and there might be an old version of either sbt or Scala which could be built with what we currently have in Debian. But this is quite a lot of work, and I feel no one is willing to do it now -- perhaps that Scala thing is quite peculiar and we would need someone with time and high skills. In September I exchanged a few emails with a colleague of Steffen, who knows Scala. While he helped a lot on understanding some aspects of the language, he does not know about the Debian workflow -- which is plainly understandable -- and thus we are, so far, left with the current issue. Maybe we should see if there is another framework for concurrent programming in pure Java that we could fit into Snpeff by writing patches... > > Kind regards > > Andreas. > Bye, Pierre
