OSX Installation Issues - exited with status error 1

[zhemingfan]

Describe the bug

To Reproduce
Steps to reproduce the behavior:

1. After following installation instructions for blat and create a separate python virtual environment:
2. See error ...
   error.txt

Expected behavior
Complete installation of MAVIS with expected output.

Configuration
If applicable, include the mavis configuration file that was used to run the pipeline

Versions (please complete the following information):

• OS: MacOS Catalina 10.15.7
• Python Version: 3.9
• MAVIS Version: 2.0.0
• Blat/BWA Version: Latest MacOS version found at: http://hgdownload.soe.ucsc.edu/admin/exe/

Additional context
Add any other context about the problem here.

[creisle]

This looks like a compiler error. OSX uses a different compiler by default than linux distributions. Could you post the version of that? gcc --version

Did you update setuptools and pip before installing? Newer versions of those install pre-compiled binaries where possible which often allows you to bypass compilation problems

[zhemingfan]

pip install --upgrade pip setuptools prior to installation

setuptools version: 54.0.0

pip version: pip 21.0.1

Gcc version output:

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.27)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

[creisle]

MAVIS is primarily developed for linux, although I have tested it on some OSX environments. The issue here appears to be happening during installing pysam. It doesn't have a pre-compiled binary for your OS and so it attempts to compile it from scratch, but b/c OSX uses a non-standard compiler (clang instead of gcc) it is running into issues

[creisle]

Python 3.9 is super new so it might not have all the pre-compiled verisons yet, could you try with a lower python version? perhaps 3.8 or 3.7?

[creisle]

Ok I have been able to reproduce a similar error on ubuntu with python3.9 + pysam so it may not be a OS issue. We will look into this further. @calchoo we froze pysam at 0.15.1 because of breaking changes in 0.15.2, do you remember what those were? have they been fixed?

[zhemingfan]

Okay great thanks!