There seems to be a Python incompatibility issue between Medaka and Protobuf. Medaka runs on Python 3.5 and 3.6, but the latest Protobuf requires >=3.7. The issue is (hopefully) addressed in this pull request. The two related bugs are copied below in case anybody runs into them, and the fix is in the pull request.
Protobuf error
protobuf requires Python '>=3.7' but the running Python is 3.6.9
The command '/bin/sh -c pip3 install medaka==0.12.0' returned a non-zero code: 1
SyntaxError
File "/tmp/pip-build-mef35aut/pyfaidx/.eggs/setuptools_scm-7.0.2-py3.6.egg/setuptools_scm/__init__.py", line 5
from __future__ import annotations
^
SyntaxError: future feature annotations is not defined
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-mef35aut/pyfaidx/
The command '/bin/sh -c pip3 install medaka==0.12.0' returned a non-zero code: 1
There seems to be a Python incompatibility issue between Medaka and Protobuf. Medaka runs on Python 3.5 and 3.6, but the latest Protobuf requires >=3.7. The issue is (hopefully) addressed in this pull request. The two related bugs are copied below in case anybody runs into them, and the fix is in the pull request.
Protobuf error
SyntaxError