pip fails to build MSBWT

Question

[jwalewski]

Hello all,

I am trying to install msbwt (https://github.com/holtjma/msbwt) on a WSL so that I can then use FMLRC (https://github.com/holtjma/fmlrc). Although msbwt recommends that it be installed with easy_install that package management software seems to be deprecated. Given that it's seemingly available with pip I attempted to use it to install msbwt, however I kept getting the following errors (the whole message is long, so I'll have it in a comment, but here's the gist):

pip install msbwt
Collecting msbwt
  Using cached msbwt-0.3.0.tar.gz (1.9 MB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: pysam in /mnt/c/ultimate/other_software/miniconda3/lib/python3.9/site-packages (from msbwt) (0.18.0)
Requirement already satisfied: numpy in /mnt/c/ultimate/other_software/miniconda3/lib/python3.9/site-packages (from msbwt) (1.21.5)
Building wheels for collected packages: msbwt
  Building wheel for msbwt (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /mnt/c/ultimate/other_software/miniconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-z67t275r/msbwt_33b8b18c49004572b0dffbc821bac183/setup.py'"'"'; __file__='"'"'/tmp/pip-install-z67t275r/msbwt_33b8b18c49004572b0dffbc821bac183/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-rxycpizo
       cwd: /tmp/pip-install-z67t275r/msbwt_33b8b18c49004572b0dffbc821bac183/

... More lines (238 total)

------------
ERROR: Failed building wheel for msbwt
  Running setup.py clean for msbwt
Failed to build msbwt
Installing collected packages: msbwt
    Running setup.py install for msbwt ... error
    ERROR: Command errored out with exit status 1:
     command: /mnt/c/ultimate/other_software/miniconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-z67t275r/msbwt_33b8b18c49004572b0dffbc821bac183/setup.py'"'"'; __file__='"'"'/tmp/pip-install-z67t275r/msbwt_33b8b18c49004572b0dffbc821bac183/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-hx_1kqas/install-record.txt --single-version-externally-managed --compile --install-headers /mnt/c/ultimate/other_software/miniconda3/include/python3.9/msbwt
         cwd: /tmp/pip-install-z67t275r/msbwt_33b8b18c49004572b0dffbc821bac183/

... (Again another 238 lines of output)

Let me know if anything needs more clarification - I am very new to the field (I am an undergraduate doing research with my professor!) Thanks all for your help!

[GenoMax]

Msbwt and its modules have been tested under Python 2.7.

Make sure you have python v.2.7 (or better) installed.You are likely getting those errors since the install process is trying to use default python v.3.9.