Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

>>
>>> Also, I notice that pysam bundles htslib, bcftools and samtools C code.
>>> Hopefully it should be straightforward enough to remove htslib as there
>>> are install instructions, I'm not sure about the other two. This
>>> shouldn't block the patch here, but would you mind taking a look?
>>> http://pysam.readthedocs.io/en/latest/installation.html#installation
>> I had a go at this, and also enabled tests since I was reading the build
>> system anyway. Samtools and bcftools does not seem possible to un-bundle
>> at this time, but htslib was straightforward.
> OK. I don't think it needs to be propagated though, right? Also, would 
> you mind separating the change to modify-phases syntax and unbundling of 
> htslib into two patches please? Other than that this whole series LGTM.

Modify-phases is now a separate patch. Htslib is propagated because it
is included by the installed samtools and bcftools headers; at least one
of pysams dependencies failed to build when it was a regular input.

I added some comments and other cosmetic changes. Updated patch below.

Cheers!