[Debian-med-packaging] Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

[olivier sallou]

Le lun. 12 déc. 2016 à 08:34, Andreas Tille <tille at debian.org> a écrit :

> Hi Olivier,
>
> On Mon, Dec 12, 2016 at 07:01:19AM +0000, olivier sallou wrote:
> > I have uploaded biojava, do you still need i have a look? Seems sasha did
> > the job.. :-)
>
> Yes, thanks to Sascha for taking over.
>
> For me currently the most urgend Java tasks are:
>
>  * Upgrade BioJava 1.x series to its latest version
>
ithnk it is a difficult task (reason I did not update before). As version
is quite old and nobody requested for an upgrade, I think we should keep
old version or drop if no program depends on it

>  * Decide whether we can drop BioJava 3 since it conflicts
>    with latest Jmol
>
keeping all old releases in sync with new dependencies can be quite time
consuming. It is indeed worth the effort as new releases come out?

 * Make BioJava 4.x compatible with Jmol 14
>
if upstream is working on it, let's wait if something comes.
Is latest jmol in experimental?


>  * Care for latest version of Jalview
>
> There are two threads about Jmol on the Debian Med list currently and the
> latest status is here[1].  It would be helpful to hear your opinion about
> BioJava.
>
> Kind regards
>
>       Andreas.
>
> [1] https://lists.debian.org/debian-med/2016/12/msg00103.html
>
> --
> http://fam-tille.de
>
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