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

[Andreas Tille]

Hi Charles,

On Mon, Nov 04, 2013 at 10:04:05PM +0900, Charles Plessy wrote:
> 
> Here are extra comments:
> 
>  - for samtools, we need to ensure that this upcoming version 0.2, which feels
>    like being actually like a 2.0, is not breaking backwards compatibility.  If
>    it would be the case, then we should make a samtools0.2 package.

Yep.  Some unit tests might be helpful here.  I wonder whether bcftools,
htslib and samtools might depend somehow from each other or whether all
could be uploaded independently.
 
>  - In the meantime, I recommend to avoid the rc releases of samtools in Unstable,
>    so that you can concentrate of getting Rsamtools and r-bioc-cummerbund up to
>    date in the short term.  I think that we are in a situation where we are able to do
>    the extra work in case a severe flaw is found in the samtools source, which would
>    need to correct all related packages.

OK.  I'll describe the situation in README.source and will upload Rsamtools.
 
>  - In the longer term, we need to package the bcftools and the htslib.
> 
>  - If these packages do not provide dynamic libraries, it may be a good time
>    for us (me ?) to ask for it.

Perhaps it is a good idea to ask *now* since ~rc? means some possible
changes for the release are possible.  If we might delay an according
question it might be harder to wait for the next release.

>    In parallel or after, somebody (you ?) needs to
>    ask the Rsamtools upstream to migrate to samtools 0.2, and take the opportunity
>    to use the libraries directly.

I'll do so once the package might have hit unstable / or refused by
ftpmaster for this reason.
 
> I will help with the packaging work related to the 0.2 version of samtools.

Great.

Kind regards

       Andreas. 

-- 
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