pip3 install  --user -r requirements.txt
Collecting cython>=0.22 (from -r requirements.txt (line 1))
  Using cached Cython-0.24-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pysam>=0.9.0 (from -r requirements.txt (line 2))
  Using cached pysam-0.9.0.tar.gz
    Complete output from command python setup.py egg_info:
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for ranlib... ranlib
    checking how to run the C preprocessor... gcc -E
    checking for grep that handles long lines and -e... /usr/bin/grep
    checking for egrep... /usr/bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking for stdlib.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking for sys/param.h... yes
    checking for getpagesize... yes
    checking for working mmap... yes
    checking for gmtime_r... yes
    checking for zlib.h... yes
    checking for inflate in -lz... yes
    checking for curl_easy_pause in -lcurl... yes
    checking for CCHmac... yes
    configure: creating ./config.status
    config.status: creating config.mk
    config.status: creating config.h
    # pysam: htslib mode is separate
    # pysam: htslib configure options: --enable-libcurl
    # pysam: libcurl of builtin htslib has been enabled, adding shared libcurl and libcrypto
    Traceback (most recent call last):
      File "<string>", line 20, in <module>
      File "/private/var/folders/6h/z3xbm5ws0x13tjt52yqhw2ww0000gn/T/pip-build-myobxv_r/pysam/setup.py", line 290, in <module>
        .format(fn))
    ValueError: no cython installed, but can not find pysam/chtslib.c.Make sure that cython is installed when building from the repository

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/6h/z3xbm5ws0x13tjt52yqhw2ww0000gn/T/pip-build-myobxv_r/pysam
You are using pip version 7.1.2, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.