Marius Bakke <mbakke@fastmail.com> writes:

> 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.

Oops, found a spelling error in the previous patch. Fixed.