Progress of Snpeff packaging (Was: Re: /usr/bin/picard Re: bcbio will need another while - needs gatk)
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
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