[Debian-med-packaging] Convenience code copy of samtools and tabix in r-bioc-rsamtools.

[Andreas Tille]

Hi Charles,

On Wed, Oct 30, 2013 at 06:43:03PM +0900, Charles Plessy wrote:
> Le Wed, Oct 30, 2013 at 06:38:39PM +0900, Charles Plessy a écrit :
> > 
> > Ah, and I see libbcf.a as well.  This one can be build from samtools.
> > Quick-and-dirty way would be to put it in libbam-dev, otherwise we need to make
> > a new package with a trip to the NEW queue.
> 
> Hmmm, and I see samtools 0.2.0~rc3 on GitHub, with the following in the README:
> 
>     The original samtools package has been splitted into three separate but tightly coordinated projects:
>     
>         htslib: C-library for handling high-throughput sequencing data
>         samtools: mpileup and other tools for handling SAM, BAM, CRAM
>         bcftools: calling and other tools for handling VCF, BCF
> 
> If there is anybody (newcomers welcome !) who would like to contribute on this:
> the more the merrier !

Thanks for these useful hints.  As you might have read in my additional
posting to the ITP bug and BioConductor maintainers there will be some
additional work to do before we will be able to upload this package.

Meanwhile these "origin of binary files" issues (which are not only
those simple Rdata issues) will be clarified we could try to tackle the
technical challenges you did mention.  I'd naively say that the package
comes with unit tests and we could just simply try and follow the method
I used in the patch to link against Debian packaged zlib.

I will be way less active the next four days (short vacation without the
need to send an official vac message) - so if somebody likes to test
this I'd be very happy.

Kind regards

        Andreas.

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