ksw2 library - nobody else at it, right?

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ksw2 library - nobody else at it, right?

Steffen Möller
Hello,

I was about to help out the minimap2's "mappy" python interface which
has a dependeny on https://github.com/lh3/ksw2 that to my understanding
yet did not find entry to our distribution.

Nobody is working on this, right? I'd then come up with something.

Best,

Steffen

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Re: ksw2 library - nobody else at it, right?

Andreas Tille-5
Hi Steffen,

On Thu, May 14, 2020 at 05:29:15PM +0200, Steffen Möller wrote:
> I was about to help out the minimap2's "mappy" python interface which
> has a dependeny on https://github.com/lh3/ksw2 that to my understanding
> yet did not find entry to our distribution.
>
> Nobody is working on this, right? I'd then come up with something.

Ahhh, yes, seems I missed this real point of the build issue.
Thanks for spotting and please push that package if you have
time for it.

Kind regards

     Andreas.

--
http://fam-tille.de

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Re: ksw2 library - nobody else at it, right?

Andreas Tille-5
Hi Steffen,

could you push to Salsa soon?

Kind regards

      Andreas.

On Thu, May 14, 2020 at 05:50:46PM +0200, Andreas Tille wrote:

> Hi Steffen,
>
> On Thu, May 14, 2020 at 05:29:15PM +0200, Steffen Möller wrote:
> > I was about to help out the minimap2's "mappy" python interface which
> > has a dependeny on https://github.com/lh3/ksw2 that to my understanding
> > yet did not find entry to our distribution.
> >
> > Nobody is working on this, right? I'd then come up with something.
>
> Ahhh, yes, seems I missed this real point of the build issue.
> Thanks for spotting and please push that package if you have
> time for it.
>
> Kind regards
>
>      Andreas.
>
> --
> http://fam-tille.de
>
>

--
http://fam-tille.de

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Re: ksw2 library - nobody else at it, right?

Steffen Möller
Hi Andreas,

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. 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.

Thanks,

Steffen


On 14.05.20 23:18, Andreas Tille wrote:

> Hi Steffen,
>
> could you push to Salsa soon?
>
> Kind regards
>
>        Andreas.
>
> On Thu, May 14, 2020 at 05:50:46PM +0200, Andreas Tille wrote:
>> Hi Steffen,
>>
>> On Thu, May 14, 2020 at 05:29:15PM +0200, Steffen Möller wrote:
>>> I was about to help out the minimap2's "mappy" python interface which
>>> has a dependeny on https://github.com/lh3/ksw2 that to my understanding
>>> yet did not find entry to our distribution.
>>>
>>> Nobody is working on this, right? I'd then come up with something.
>> Ahhh, yes, seems I missed this real point of the build issue.
>> Thanks for spotting and please push that package if you have
>> time for it.
>>
>> Kind regards
>>
>>       Andreas.
>>
>> --
>> http://fam-tille.de
>>
>>

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Re: ksw2 library - nobody else at it, right?

Andreas Tille-5
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

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Re: ksw2 library - nobody else at it, right?

Andreas Tille-5
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

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Re: ksw2 library - nobody else at it, right?

Andreas Tille-5
Hi again,

anybody up for contacting upstream as a first step?

Kind regards

     Andreas.

On Tue, Jun 09, 2020 at 05:28:28PM +0200, Andreas Tille wrote:

> 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
>
>

--
http://fam-tille.de

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Re: ksw2 library - nobody else at it, right?

Andreas Tille-5
Hi,

I find more and more packages in need of python3-mappy which is
build by minimap2 but to succeed here ksw2 is needed.  It would
be great if somebody would take over here.

Kind regards

        Andreas.

On Mon, Jun 15, 2020 at 09:08:56AM +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