Re: Nextflow - have just used it on our HPC cluster and liked it

[Pierre Gruet]

Hi Andreas,

Le 09/05/2023 à 18:36, Andreas Tille a écrit :

Hi Pierre,

Am Mon, May 08, 2023 at 10:50:54PM +0200 schrieb Pierre Gruet:

It is very nice to hear from you on Nextflow, this is a motivation booster
for the packaging!

+1

I have indeed packaged many dependencies, and if I remember correctly I had
two issues at this step:
- kryo 5.x is needed although we have libkryo-java/2.7 in Debian, which
cannot be upgraded to version 5.x as it would break gradle (!). So we need a
dedicated src:kryo5 package, I began doing it but took a break for whatever
reason;

If we need two versions of kryo it needs passing new - thus you can upload
it at any time, thought.

True, yes.

- more annoying: I need groovy 3.x and in Debian we have groovy 2.4.21. I
tried to package it but met some antlr4 issues on which I have to spend more
time.

I think reworking on this will be a good task after the release of Bookworm.
I can try again and post possible issues here.

May be groovy can be upgraded in experimental to version 3.x?

Possibly I have been unclear there, sorry: when trying to build groovy 3.x, I had issues linked to antlr4 which prevented me from completing the whole build, so I am not even ready to propose a working upgrade of groovy... but since then, I have met other issues with antlr4 in other packages and could circumvent some of them, so I guess I should just try again as I now have more experience, and possibly coordinate with other interested people in debian-java.

Thanks a lot for working on all these dependencies!

And thanks for advising! :)

Kind regards
      Andreas.

Best,

--
Pierre

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