UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 679: ordinal not in range(128)

[juanesarango]

• toil_container version: 1.1.7
• Python version: 2.7.15
• Operating System: "Red Hat Enterprise Linux 8.6 (Ootpa)"

Getting this error:

Traceback (most recent call last):
  File ".../venv__toil_brass__v1.0.2/bin/toil_brass", line 8, in <module>
    sys.exit(main())
  File ".../venv__toil_brass__v1.0.2/lib/python2.7/site-packages/toil_brass/cli.py", line 23, in main
    commands.main()
  File ".../venv__toil_brass__v1.0.2/lib/python2.7/site-packages/toil_brass/commands.py", line 453, in main
    options = get_parser().parse_args()
  File ".../venv__toil_brass__v1.0.2/lib/python2.7/site-packages/toil_container/parsers.py", line 226, in parse_args
    validators.validate_singularity(**validate_kwargs)
  File ".../venv__toil_brass__v1.0.2/lib/python2.7/site-packages/toil_container/validators.py", line 16, in validate_singularity
    _validate_image(singularity_call, image, volumes, working_dir)
  File ".../venv__toil_brass__v1.0.2/lib/python2.7/site-packages/toil_container/validators.py", line 31, in _validate_image
    call(image, cmd, check_output=True, **kwargs)
  File ".../venv__toil_brass__v1.0.2/lib/python2.7/site-packages/toil_container/containers.py", line 134, in singularity_call
    return output.decode()
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 679: ordinal not in range(128)

As singularity call is not returning a binary encoded output. This might be related with default encoding of the host.

Fixed by specifying explicitly the encoding:

return output.decode("utf-8")

[ddomenico]

Testing a new branch with utf-8 explicitly defined in decode(): https://github.com/papaemmelab/toil_container/tree/v1.1.8