pip install pysam failed

[GraceTan]

Hi,

I followed the instructions of the README.md file, and I am able to install pysam using pip install. It is complaining about a missing file os/lzma_stub.h. I am doing this on a Mac. Thanks.

/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/private/var/folders/zh/h1rbt3zd68x8ds9_t0bdz_vh0000gp/T/pip-build-kVYTDR/pysam/htslib -I/private/var/folders/zh/h1rbt3zd68x8ds9_t0bdz_vh0000gp/T/pip-build-kVYTDR/pysam/samtools -I/private/var/folders/zh/h1rbt3zd68x8ds9_t0bdz_vh0000gp/T/pip-build-kVYTDR/pysam/samtools/lz4 -I/private/var/folders/zh/h1rbt3zd68x8ds9_t0bdz_vh0000gp/T/pip-build-kVYTDR/pysam/bcftools -I/private/var/folders/zh/h1rbt3zd68x8ds9_t0bdz_vh0000gp/T/pip-build-kVYTDR/pysam/pysam -I/private/var/folders/zh/h1rbt3zd68x8ds9_t0bdz_vh0000gp/T/pip-build-kVYTDR/pysam -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.macosx-10.13-x86_64-2.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
    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
    

[pjshort]

Specifying pip install pysam==0.13 (rather than 0.14) worked for me, so maybe give that a try!