Re: Nextflow - have just used it on our HPC cluster and liked it
On Tue, 2023-05-09 at 22:24 +0200, Pierre Gruet wrote:
> 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.
groovy is definitly a Java tool needed for many java packages, you
should get help/interest from debian-java for this.
I already had issue with previous groovy versions and antlr too,
upgrades breaking stuff....
Olivier
>
> >
> > Thanks a lot for working on all these dependencies!
>
> And thanks for advising! :)
>
> >
> > Kind regards
> > Andreas.
> >
>
> Best,
>
> --
> Pierre
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
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