Hi,
is anybody up for this challenge? This is needed for the minimap2
Python module which we need for other packages.
Kind regards
Andreas.
On Fri, May 15, 2020 at 02:30:02PM +0200, Andreas Tille wrote:
> Hi Steffen,
>
> On Fri, May 15, 2020 at 02:39:51AM +0200, Steffen Möller wrote:
> > I am happy that you asked - it is here
> > https://salsa.debian.org/med-team/ksw2
> >
> > Sadly not a problem of that library which features the same files that
> > are also distributed with minimap2, just as an older version in the
> > separate ksw2 repository if I am not erroneous.
>
> Yes, file ksw2_exts2_sse.c seems to be older than in the code copy in
> minimap2.
>
> > We need to find the
> > problem within the minimap2 package, I am afraid. Was looking for a
> > while now - thought multiple times that I had it - but ... sigh.
> >
> > That ksw2 library needs some love by upstream and I suggest to avoid
> > packaging it for now. Also, it does not ship with a license and comes
> > with the sources of a journal publication - er - have a look.
>
> Besides that I agree that it should be sorted out with upstream I
> think the proper action would be:
>
> 1. Sort out the code update with upstream
> 2. Ask upstream for a proper release
> 3. Fix the build system I've invented to get a proper library
>
> Regarding the last item: I have added extremely rough automake stuff to
> the packaging. The idea was that I want a proper library with static and
> dynamic library. However, my automake skills are limited. Here are the
> flaws:
>
> 1. Proper check for zlib is needed (see the dirty hack in d/rules)
> 2. There is no propagation of HAVE_KALLOC definition (no idea why)
> 3. Check and use parasail
> 4. May be package gaba (whatever this might be and check and link
> against this)
>
> Finally I took over the simde patch from minimap2. Unfortunately I have
> no idea how to add this to the linker. This has also be done inside
> my weak attempt of automake. (If you comment the simde patch the package
> at least builds.)
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
