Command errored out with exit status 1: Python setup.py [...] When trying to install Pysam

Question

I have been troubleshooting this issue for several days now and have had to draw the conclusion that i need help from you guys!

Info: Python version: 3.8.2 Pip version: 20.0.2

Updated Setuptools Setuptools wheel Python-language-server

Installing module using pip with following commands python -m pip install pysam or python -m pip install C:\Users\NDSNIVE\Downloads\pysam-master.zip

Full error code

ERROR: Command errored out with exit status 1:
 command: 'c:\program files\python38\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\NDSNIVE\\AppData\\Local\\Temp\\pip-req-build-_mdk7oi0\\setup.py'"'"'; __file__='"'"'C:\\Users\\NDSNIVE\\AppData\\Local\\Temp\\pip-req-build-_mdk7oi0\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\NDSNIVE\AppData\Local\Temp\pip-req-build-_mdk7oi0\pip-egg-info'
     cwd: C:\Users\NDSNIVE\AppData\Local\Temp\pip-req-build-_mdk7oi0\
Complete output (23 lines):
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
'.' is not recognized as an internal or external command,
operable program or batch file.
'.' is not recognized as an internal or external command,
operable program or batch file.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\NDSNIVE\AppData\Local\Temp\pip-req-build-_mdk7oi0\setup.py", line 241, in <module>
    htslib_make_options = run_make_print_config()
  File "C:\Users\NDSNIVE\AppData\Local\Temp\pip-req-build-_mdk7oi0\setup.py", line 68, in run_make_print_config
    stdout = subprocess.check_output(["make", "-s", "print-config"])
  File "c:\program files\python38\lib\subprocess.py", line 411, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "c:\program files\python38\lib\subprocess.py", line 489, in run
    with Popen(*popenargs, **kwargs) as process:
  File "c:\program files\python38\lib\subprocess.py", line 854, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "c:\program files\python38\lib\subprocess.py", line 1307, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] Den angivne fil blev ikke fundet
# pysam: htslib configure options: None
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Answer 1

pysam is only compatible with these operating systems (from pypi), so not windows:

Operating System

MacOS
POSIX
Unix