failed to build pysam (CAVA-1.2.3)

[mmqjs]

Hi,

I recently tried installing CAVA-1.2.3 and received an error related to pysam. I copied some of the installation text below. Could you help me?

Building wheels for collected packages: pysam, wrapt
  Building wheel for pysam (setup.py): started
  Building wheel for pysam (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /home/CAVA-1.2.3/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-z1DeHE/pysam/setup.py'"'"'; __file__='"'"'/tmp/pip-install-z1DeHE/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-aRD_gL
       cwd: /tmp/pip-install-z1DeHE/pysam/
  Complete output (74 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-2.7
  creating build/lib.linux-x86_64-2.7/pysam
  copying pysam/__init__.py -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/Pileup.py -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/version.py -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/namedtuple.py -> build/lib.linux-x86_64-2.7/pysam
  creating build/lib.linux-x86_64-2.7/pysam/include
  copying pysam/include/__init__.py -> build/lib.linux-x86_64-2.7/pysam/include
  creating build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/__init__.py -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  creating build/lib.linux-x86_64-2.7/pysam/include/samtools/bcftools
  copying samtools/bcftools/__init__.py -> build/lib.linux-x86_64-2.7/pysam/include/samtools/bcftools
  creating build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
  copying samtools/win32/__init__.py -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
  creating build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/__init__.py -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying pysam/csamtools.pxd -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/ctabix.pxd -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/cvcf.pxd -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/TabProxies.pxd -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/tabix_util.h -> build/lib.linux-x86_64-2.7/pysam
  copying pysam/pysam_util.h -> build/lib.linux-x86_64-2.7/pysam
  copying samtools/bam_endian.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/klist.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/razf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/bam.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/kstring.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/bgzf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/faidx.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/pysam.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/khash.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/kprobaln.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/sam_header.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/kseq.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/errmod.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/knetfile.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/bam2bcf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/kaln.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/sam.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/bam_tview.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/ksort.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/sample.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
  copying samtools/bcftools/kmin.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/bcftools
  copying samtools/bcftools/prob1.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/bcftools
  copying samtools/bcftools/bcf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/bcftools
  copying samtools/win32/zconf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
  copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
  copying samtools/win32/zlib.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
  copying tabix/bam_endian.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/tabix.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/kstring.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/bgzf.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/pysam.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/khash.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/kseq.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/knetfile.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  copying tabix/ksort.h -> build/lib.linux-x86_64-2.7/pysam/include/tabix
  running build_ext
  building 'pysam.csamtools' extension
  creating build/temp.linux-x86_64-2.7
  creating build/temp.linux-x86_64-2.7/pysam
  creating build/temp.linux-x86_64-2.7/samtools
  creating build/temp.linux-x86_64-2.7/samtools/bcftools
  creating build/temp.linux-x86_64-2.7/samtools/misc
  x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-1x6jhf/python2.7-2.7.18~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.7/pysam/csamtools.o
  pysam/csamtools.c:4:10: fatal error: Python.h: No such file or directory
      4 | #include "Python.h"
        |          ^~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pysam
  Running setup.py clean for pysam
  Building wheel for wrapt (setup.py): started
  Building wheel for wrapt (setup.py): finished with status 'done'
  Created wheel for wrapt: filename=wrapt-1.12.1-py2-none-any.whl size=19553 sha256=a3d90ada737479b9142d1c60ac90adcff78b0a3b5f27f2a97de15985b5810404
  Stored in directory: /tmp/pip-ephem-wheel-cache-KxCIam/wheels/5b/d8/8e/81a83cb5321b940a954996f5b57fddc8976e712b3ac3a1a54b
Successfully built wrapt
Failed to build pysam
ERROR: pytest-cov 2.10.0 has requirement pytest>=4.6, but you'll have pytest 3.0.7 which is incompatible.
Installing collected packages: appdirs, Cython, enum34, pycodestyle, configparser, mccabe, pyflakes, flake8, pyparsing, six, packaging, pep8, py, singledispatch, backports.functools-lru-cache, wrapt, lazy-object-proxy, astroid, futures, isort, pylint, pysam, setuptools, pytest, coverage, pytest-cov, mando, flake8-polyfill, colorama, radon, docutils, typing, MarkupSafe, Jinja2, Pygments, imagesize, snowballstemmer, urllib3, certifi, chardet, idna, requests, pytz, babel, sphinxcontrib-websupport, alabaster, sphinx, greenlet, gevent
    Running setup.py install for pysam: started
    Running setup.py install for pysam: finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /home/CAVA-1.2.3/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-z1DeHE/pysam/setup.py'"'"'; __file__='"'"'/tmp/pip-install-z1DeHE/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-FQc1uk/install-record.txt --single-version-externally-managed --compile --install-headers /home/CAVA-1.2.3/env/include/site/python2.7/pysam
         cwd: /tmp/pip-install-z1DeHE/pysam/
    Complete output (75 lines):