comparison tests/test_imgt.py @ 57:33412e85e669 draft

"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"

56:7ae6b6b5d890

        clonality_method
    ]
    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                  "-v", f"{sample}:{sample}",
                  "-w", str(working_dir),
                  get_container()] + cmd
    with open(temp_dir / "stderr", "wt") as stderr_file:
        with open(temp_dir / "stdout", "wt") as stdout_file:
            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
                           stderr=stderr_file, check=True)

57:33412e85e669

        clonality_method
    ]
    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                  "-v", f"{sample}:{sample}",
                  "-w", str(working_dir),
                  # Run as current user which allows deletion of files.
                  # It also mitigates some security considerations
                  "-u", f"{os.getuid()}:{os.getgid()}",
                  # Run with default seccomp profile to mitigate mitigation slowdown
                  # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
                  "--security-opt", "seccomp=unconfined",
                  get_container()] + cmd
    with open(temp_dir / "stderr", "wt") as stderr_file:
        with open(temp_dir / "stdout", "wt") as stdout_file:
            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
                           stderr=stderr_file, check=True)