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