On 24/09/16 01:56, Marius Bakke wrote:
Ben Woodcroft <b.woodcr...@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.
Thanks.
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.
Ah, I see. Can this be avoided with patchelf?
ben
