Can't install pysam with pip in Python 3.6

Question

Macbook Mac OSX 10.12.6 Python 3.6.2 cython 0.28.5 pip 18.0

I'm trying to install pysam:

pip3 install pysam

It keeps hitting an error at:

creating build/temp.macosx-10.6-intel-3.6/htslib/cram
htslib/cram/cram_io.c:63:10: fatal error: 'os/lzma_stub.h' file not found
#include "os/lzma_stub.h"
         ^~~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' failed with exit status 1

Seems like this issue, this, and this were version issues. But I've tried pip3 install pysam==0.13 and 0.14 and 0.15 with the same results.

Suggestions?

I really don't want to deal with installing conda...

Answer 1

Clearly, you are missing lzma, which is now part of xz library (https://tukaani.org/xz/). Install that and see if it works. In OSX, you can install it using homebrew: brew install xz.

Another option is to install htslib (http://www.htslib.org/download/), or samtools (can be found in the htslib url).

Answer 2

My mistake! pip3 install pysam==0.13 actually DOES work. Just leaving this here for posterity.