Tierpsy Docker: investigate whether running the docker container as root is necessary

[taylorreiter]

In the Snakefile, we're currently running the docker container as root user:

rule run_tierpsy_tracker:
    ...
    shell:
        """
        docker exec -u root \
        ...
        """

In #6, @keithchev asked:

Is -u root necessary? afaik it's a bad practice to run containers as root (though I think it's also common, so probably nbd here)

It was necessary in my testing, but that was before I added umask 000 to the beginning of the bash code run by docker exec. I need to investigate whether it is still necessary or can be run without this.

[taylorreiter]

Ok I tried this out on a toy snakefile running the same docker exec command and found that -u root is necessary. Without it, I get:

Traceback (most recent call last):
  File "/home/tierpsy_user/.local/bin/tierpsy_process", line 33, in <module>
    sys.exit(load_entry_point('tierpsy', 'console_scripts', 'tierpsy_process')())
  File "/tierpsy-tracker/tierpsy/processing/processMultipleFilesFun.py", line 133, in tierpsy_process
    processMultipleFilesFun(**vars(args))
  File "/tierpsy-tracker/tierpsy/processing/processMultipleFilesFun.py", line 117, in processMultipleFilesFun
    files_checker = CheckFilesForProcessing(**check_args)
  File "/tierpsy-tracker/tierpsy/processing/CheckFilesForProcessing.py", line 46, in __init__
    self.mask_dir_root = _makeDirIfNotExists(mask_dir_root)
  File "/tierpsy-tracker/tierpsy/processing/CheckFilesForProcessing.py", line 41, in _makeDirIfNotExists
    os.makedirs(fname)
  File "/usr/local/lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/DATA/local_drive/tmp_tierpsy_out/masks'