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Re: Packaging SMALT for Debian

Hi Hannes,

On Wed, Apr 09, 2014 at 10:06:18AM +0100, Hannes Ponstingl wrote:
> Hi Andreas,
> Fine with me if you would like to forward our conversation to the list.

Done.  Thanks for the permission.

> The attached patch should fix the glitch with the dependencies of
> bam_cigar_test.py you correctly identified.

Thanks for the patch.  I'll try to apply this.  However, as I said in my
previous mail, the problem is not to find a clue in Makefile.am but to
rather create a valid Makefile.in out of it with recent automake which
is on one hand a bit picky about some definitions and on the other hand
creates a broken makefile trying to call `python /bin/bash` which for
sure is bound to fail.

> Perhaps I should try and package smalt myself but I have no
> experience with this and currently not much time.

I think the basic things are done and the things to do are quite
clear from a packaging point of view.  The current problem is the
non-working automake stuff ... at least when using

$ automake --version
automake (GNU automake) 1.14.1

I think the fastest (not necessarily cleanest) solution would be if you
could apply the patch you sended to your upstream source and create a
new upstream tarball (featuring a valid Makefile.in).  Another solution
could be if I would ask on a Debian list where people are way more
skilled with automake than me.

The next step will be to package bambamc library anyway so the problem
will become invisible.

However, for sure you can also become involved in the packaging and we
are providing support for newcomers in the Debian Med team[1] which
worked quite well in the past.  So in case you might face some spare
time cycles you are more than welcome to become involved in the

Kind regards


[1] https://wiki.debian.org/DebianMed/MoM


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